I haven't used github in a while, when does an unclean merge happen? When two people merge their branches at the same time?
We see this often with lockfiles (someone updates a dep, someone else adds a new dependency; the merge is a new dependency to a version of the dependency that no longer exists), or version numbers that get incremented (each author increments once; the second merge, git will consider it the same add on both sides, and not a conflict, so the result it original_version+1, when it should be original_version+2).