QB Issue Resolution:

Penalties and interest are not typically accrued through the tax function, of course. That means you issue the check, or pay it by credit card, or accrue it through AP, just like any other payable.

Resolution for Issue 'CRA penalty & interest on GST account' available: Yes (Solved).
Source: Intuit Community forum.

CRA penalty & interest on GST account: 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 GST
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Error Recovery for GST [Canada]
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