QB Issue Resolution:

is it possible that you are seeing 1 entry for the employee and the 2nd for the company?  that would be correct.

Resolution for Issue 'Payroll is not calculating payroll properly. Social Security withholding and medicare withholding amounts for the employee have doubled? What is going on?' available: Yes (Solved).
Source: Intuit Community forum.

Payroll is not calculating payroll properly. Social Security withholding and medicare withholding amounts for the employee have doubled? What is going on?: 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 calculating payroll
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Error Recovery for calculating payroll [Canada]
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