Hey,
It seems you want us to give you an answer to your assignment 😉. Well, HRMS implementation attracts many issues, the first being CHANGE.
Since you have specifically asked about issues that come operational once HRMS is implemented, I will restrict myself to that.
Frankly speaking, HRMS is considered successfully implemented only if there are no technical or acceptance issues.
Any HRMS application, when finalized by an organization, requires top management's nod. This nod signifies the company is comfortable with the technology (J2EE, ASP.net, or any other), the investment asked for, the scope, and yield of the project. Once everything is okayed, then actual implementation starts.
This is the point where many companies realize the need to define employee roles more clearly. Defining the business rules in the system is the next challenge faced. Similarly, the various workflows and related escalations need the approval from top management, who then may discover the need to reengineer the organization structure for good.
All the issues arise from "the HRMS readiness" of the company.
Another aspect is Change management. The executive who used to go directly to the client's place by just informing his supervisor will now have to make a prior on-duty request or make a past attendance (subject to approval) in the system. He may feel a part of his freedom is taken away.
We have to understand that Systems (be it HRMS, CRM, or any other) bring discipline and more control of the workflows and thereby resulting in more control over people. It is the duty of HR to communicate and make people understand how these systems will help them improve their productivity and thereby the organization's profitability. The change has to be managed top-down.
Other issues that can arise are usually company and industry segment-specific.
Cheers,
Saurabh