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6 Common HR Software Problems 2025 (How to Fix?)

HR software is a critical component for your HR team. It helps automate payroll management and monitor attendance. It can also assist you in employee engagement and benefits administration. Some advanced solutions also offer data-driven decision-making by leveraging advanced AI-powered capabilities.

An HR team could face several common HR software problems, some of which include employee lack of awareness, integration-related issues, or low employee engagement. Fixing these issues is a must. Not fixing them could lead to a dip in overall productivity.

This blog will cover six common HR software problems and their solutions, including –

6 Common HR Software Problems and Solutions

1. Low Employee Engagement

Organizations often face issues related to low employee engagement. It is a well-established fact that the level of employee engagement impacts an organization’s performance and its eventual success. So, it is concerning that only 31% of employees reported being actively engaged in their work.

Similar stats concern organizations and HR teams, as effective employee engagement is critical for improving performance, maximizing employees’ capabilities and staying competitive.

Due to a lack of awareness, employees might assume that getting approvals using an HRMS would be complex. Also, there might be some issues related to payroll, wherein the people in HR find it challenging to understand and calculate payroll-related information. This could lead to dissatisfaction and trust issues.

Such a situation could have a negative impact on the working environment due to lower effectiveness and increased attrition. The solution for this common HR software problem is mentioned below.

Solution for Low Employee Engagement

First, familiarize employees with the new software in a phased manner. Provide training sessions, learning programs, and one-on-one sessions with your vendor. Your HR team would be able to maximize the benefits of your HRMS software if you have well-trained users who make fewer mistakes when configuring the software or entering data.

Comprehensive training, phased adoption, and effective utilization of learning management systems would help spread awareness while contributing to effective employee engagement.

2. Data Security

HRMS security has become one of the most sensitive issues due to the unforeseen advancement of artificial intelligence. In recent years, there has been a rise in cyber attacks, which mainly target HRMS systems, breach data, and expose confidential employee information.

Employee data, such as personally identifiable information (PII), bank account details, social security numbers, and health-related information, would be at risk in case of a data leak, compromising an employee’s personal data. This could result in fraud, doxxing, and other cybersecurity-related risks. Also, a security breach in your system could lead to ransomware attacks and access to confidential information through unregistered devices.

Hackers can also use the employee directory for targeted fishing and social attacks on your organization. You could face legal consequences if such a breach results in failure to comply with the data protection laws.

Some measures, such as multi-step verification and encryption of sensitive data, would go a long way toward ensuring the secure functioning of your HRMS. A detailed solution for this software problem is mentioned below.

Solution for Data Security

The solutions for this HR software problem are entirely based on IT support and structure, which includes using multi-factor authentication, strong passwords, having access controls on data the client needs, performing regular audits, and backing up and restoring the data. Employees need comprehensive training on cybersecurity threats to improve awareness and protect sensitive information. Consider looking at an HR software guide that can show valuable benefits and features that make it easier to follow data protection laws.

3. Ineffective Project Management

Addressing ineffective project management is essential. Well-functioning core HRMS platform is very important for successful project management and execution. It includes efficient resource allocation, enhances communication, and supports data-driven decision-making.

When HR software malfunctions or has errors, it affects the project execution, putting the technical teams under high stress to fix the glitches. These malfunctions can be due to system downtime, data integration problems, login issues, etc. Organizations must maintain reliable software to prevent errors or malfunctions. Such errors could affect the functioning of the project and its management. Here’s the solution for this issue.

Solution for Ineffective Project Management

Organizations can adapt to strategic solutions to troubleshoot and solve the issues that arise. This can be done by choosing reliable, scalable, and supportable HR software that can adapt to increased user loads and support 24/7 assistance. Also, regular maintenance should be planned with seamless data integration, which backs up the data and has recovery plans if needed. Lastly, working closely with your vendor would help resolve such issues promptly.

4. Reducing HR Manual Administrative Tasks

HR administration tasks like managing employee time-sheets and attendance, approving leaves and analyzing KPIs would take a lot of time if your HRMS malfunctions.

This could result in increased employee turnover, decreased employee engagement, and reduced overall productivity. You do not want to be in a situation where employees cannot apply for leave, attend training, or perform tasks on their ESS portal.

This creates a negative impression of the organization in the market. The solution for this common HR software problem is mentioned below.

Solution for Reducing HR Manual Administrative Tasks

Selecting the right HRMS software can automate all of these tasks, increase the efficiency of HR processes, and enhance the overall work environment. When the software is error-free, employees can focus on their daily work, saving HR professionals and employees time. The software will streamline HR tasks, allowing managers to make strategic decisions for even the fastest-growing organizations. This will lead to healthy and satisfied employees with work-life balance.

5. Integration Issues

Integration issues are some of the common challenges faced by HR software. In a dynamic, fast-paced environment where people work across multiple countries and comply with a variety of regulations, integration issues could be particularly tricky to resolve. Add to that a mix of remote, in-office, and hybrid workers who work in different shifts, and the problem becomes an immediate concern.

Challenges related to integrations result in a number of difficulties for employers and employees.

Employers find it more challenging to comply with regional and national regulations. They also find it difficult to make data-driven decisions, as a lack of integration could delay employee information access.

Employees find it harder to access their tax statements on time, review their performance, and be aware of different labor laws, because of a lack of timely resources and a prompt response due to integration-related issues.

Integration issues such as inaccurate data, incompatible systems, and data-security concerns could result in errors in payroll calculation, unintentional mismanagement of employee records, frequent glitches, and, above all, potential cybersecurity risks. The solution for this HR software problem is mentioned below.

Solution for Integration Issues

Prefer cloud-based HR software that facilitates automated payroll management and statutory compliance, helps you access employee information in real time, provides tools for touchless attendance management, and incorporates all the core HR functionalities in a single platform. Trust brands that use ISO-accredited and SOC Type 2-certified cloud data centers for guaranteed security.

6. Employee Resistance to Adoption

Adopting HR software, especially advanced software with automation capabilities, could result in employee resistance. This could cause mass unemployment.

Employee resistance could vary. They might find adapting to the new tool hard or be concerned about job security.

Employee resistance could create some serious short-term and long-term challenges.

Mistrust, frequent conflicts of interest, and a significant dip in productivity are some short-term consequences. Perpetual restlessness regarding job security and distrust towards administration due to fear of uncertainty are some of the long-term challenges. Here’s the solution to this issue.

Solution for Employee Resistance to Adoption

First, try to understand the “why” behind employee resistance. Based on your understanding, implement change-management strategies. Prepare a phased roadmap for implementing changes and make sure that they are mutually beneficial. Effective employee engagement before decision-making would make employees feel more responsible to your organization. Transparency, trust, truth, and training could really make a difference in adopting any change.

What to Look for in an HR Software Solution?

Choosing the right HR software could be tricky. But you can make it easier by creating a checklist of all your needs. Answer questions such as, “What are my needs? Why am I choosing this particular software? What are my short-term and long-term expectations from this software?” Calculating the ROI along with the cost of HR software would be advantageous as well.

While selecting a basic solution, consider factors such as payroll and compliance automation, time-tracking and attendance management features, and centralized data management. Some advanced HRMS solutions include performance management systems, employee engagement tools such as an employee self-service portal, and capabilities for data-driven decision-making.

factoHR, as an all-in-one software provider, ticks all the boxes. It is –

• Secure. It uses an ISO-accredited and SOC Type 2-certified cloud data centre.
• Integrated. It’s an all-in-one suite that covers all your HR needs from payroll management, attendance management, and time-tracking, to performance management and benefit administration.
• Empowering. factoHR provides tools such as employee self-service portal, leave management, and expense management software.
• Advanced. It provides features such as touchless attendance, facial recognition, and geofencing.

To make an informed decision, schedule a demo and explore how factoHR can simplify your HR processes.

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