The only way would be to create a separate invoice for the NSF fee

QB allocates the partial payment against all items on an invoice – you can not stop or alter that

Resolution for 'assign payments issue: 'How does QB Pro 2013 assign payments to different items on an invoice?' available: Yes.

The assign payments 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 assign payments issue yourself by looking for a resolution described in the article. If it is a complex assign payments issue or you are unable to solve the issue, you may contact us by clicking here or by using other assign payments support options.

For more information about resolving issues related to assign payments in Quickbooks/QBO or to get support for the issue 'How does QB Pro 2013 assign payments to different items on an invoice?', click the link below: