How do I fix the “Pull request can’t be updated with latest base branch changes, owner doesn’t allow modification” error?

When Strict Merge is enabled, pull requests must be updated with the latest content from the target branch before being merged. To do that, Mergify needs the permission to update the source branch of the pull request.

In certain cases, the pull request creator might not have authorized the repository owners to modify its source branch, which will block Mergify with this error. The solution is for the author of the pull request to either update manually its branch to the target branch (via a git merge or a git rebase) or to give permission for Mergify to do it as described in the GitHub documentation.

Mergify is unable to merge my pull request due to my branch protection settings

This happens usually if you limit the peopel that have the authorization to merge pull requests. GitHub does not offer any way to authorize GitHub Application (such as Mergify) to merge pull requests if you decide to set up branch protection.

You should disable this branch protection setting if you want to use Mergify merge action.

Why did Mergify seem to have merged my pull request whereas all conditions were not true?

The GitHub user interface might be misleading you in thinking that your pull request has been merged by Mergify, while it wasn’t. If your pull request A has all its commits contained in another pull request B, and if B is merged by Mergify, then A will appeared to have been merged by Mergify too. GitHub detects that A’s commits are a subset of B’s commits and therefore decides to automatically marks pull request A as merged.

Be sure that Mergify did nothing on the pull request A if it told you so in the Checks tab. This is GitHub UI magic.