Your payroll applications only support a finite number of employees, and this number is too low. If you went beyond it, there would be a negative impact.
You do not have support for multiple types of pay codes. You need to classify multiple types of pay as the same type, i.e. hourly if using paid time off. This makes it difficult to get detail on type of pay.
You need to setup multiple types of deductions/benefits as the same type. This makes it difficult to get detail on type of deductions/benefits.
Your payroll application does not support direct deposit and you do not offer it. You have to cut a check, then use third-party software to enter the data again and run it through the bank to deposit funds in employees’ accounts. This takes too much time and costs too much money.
You need to manually update tax tables as new rates are released from the Federal or State. This takes too much time, and sometimes there are errors. This has had a negative impact and has resulted in incorrect payroll taxes.
You have to track time off manually with Excel spreadsheets. You have to make manual entries for vacations, and this takes too much time.
Your payroll is not integrated with your financials and banking applications. You have to send reports back to the general ledger clerk to make transactions to track cash flow in bank reconciliation and cash flow. This takes too much time and is error-prone.
Processing payroll is complex. There are many different processes you need to go through, and it takes a long time to train someone new. Steps are missed sometimes, with negative results.
You have little flexibility with payroll runs and cannot run special bonus runs, per diem checks, or onetime checks. You have to issue and enter them manually, which takes too much time.
You have to run multiple reversing transactions through the system to void a check. You do not keep a record of voided checks, and this could cause inaccuracy.
You have to enter transactions for each employee for each pay run. This takes too much time and errors are made.