You say the merge completes succesfully with conflicts. If you solve the conflicts using version control, does the double module then dissappear?
This would be normal behaviour then. If conflicted, Mendix creates a double of the module or element. When you resolve the conflict ‘using theirs’ or ‘using mine’ the correct version is chosen and the double is removed.
https://docs.mendix.com/refguide7/using-version-control-in-the-dm#conflicts