You are asking Peer users, but let’s review:

“it was paid 5/3 (10:36 a.m. EDT)”

You sent by Thursday cut off, but there is a 2 banking date requirement.

“but fed did not receive payment for 3 more days.”

Weekend. So, Thursday Cutoff = payment reaches the bank on Monday.

“due 5/4”

To hit on Friday, […]

Resolution for 'banking date issue: 'federal tax deposits payment' available: Yes.

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

For more information about resolving issues related to banking date in Quickbooks/QBO or to get support for the issue 'federal tax deposits payment', click the link below: