QB Issue Resolution:
The SS and Medicare calculations are Year to Date calculations, so QB will automatically correct the calculations so the YTD amounts are correct for the total wagbase.
It looks like, for some reason, your ER Medicare and SS amounts had incorrect YTD amounts, so QB made a lower calculation so the YTD amounts are correct after this paycheck was created.
The “Payroll Detail Report” is useful for seeing how QB claculated each paycheck deduction. So take a look at that report and see if you find the “why” of what happened.
Resolution for Issue 'ER & EE Social Security & Medicare Taxes Differ.' available: Yes (Solved).
Source: Intuit Community forum.
ER & EE Social Security & Medicare Taxes Differ.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.Support for Employee
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