QB Issue Resolution:

I just spent over an hour on the phone to QBs support… All I needed to do when submitting my EPS was to have a digit in the ‘CIS deductions suffered’ box as well as having ’employment allowance’ ticked- I put in £0.00.

Resolution for Issue 'Employment Allowance for 2015/16 claimed but cannot submit the EPS.' available: Yes (Solved).
Source: Intuit Community forum.

Employment Allowance for 2015/16 claimed but cannot submit the EPS.: 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 Allowance
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Error Recovery for Allowance [Canada]
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