By default Git does not display files in a merge that are resolved using "mine" or "theirs" in the diff; Git simplifies the history. Unfortunately there are cases when you need to see the fact that the merge is changing what is currently in the branch even if it is a resolution of taking from an existing branch. There should be an option when viewing merge commits and during pull request to show all files impacted regardless of how they are resolved.

See https://stackoverflow.com/questions/10180751/list-merge-commits-affecting-a-file for details about this issue.