We’ve found a workaround to this issue recently. We’re using 5.6.2 with Perforce atm.
It seems to be a bug that adds engine files to the Uncontrolled Changelist when reconciling from inside the editor. When we reconciled directly from P4V there wasn’t any issue.
Response to another post with this problem.
Basically, we removed all entries in the changelist directly from the “UncontrolledChangelists.json” file in Project → Saved → SourceControl and it seems to have worked. The issue that reconciling in the engine adds all those files still exists, but this method helped us.