QB Issue Resolution:

Recieve payments for the invoice amount and group with undeposited funds, when funding and fee status are known make deposits, select your payment, make an additional entry for the fee entered as a negative amount, assign to your processing fee expense account.

Resolution for Issue 'How do I record the GoPayment 50 cent fees?' available: Yes (Solved).
Source: Intuit Community forum.

How do I record the GoPayment 50 cent fees?: 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 gopayment
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Error Recovery for gopayment [Canada]
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