You do not have support for multiple types of pay. You need to classify multiple types of pay as the same type, i.e. hourly if using paid time off, etc. 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 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 is a time-consuming and error-prone process.
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 is a time-consuming and errorprone process.