No, there is no way to override that. However if you can provide us information about dirs/files/systems where it happens, we hopefully can fix it. If it is on windows and there are case sensitivity problems, then the problem is already known, but also huge, i.e. it will hopefully be fixed eventually, but not very soon.
Most of my problems are solved now (i manually deleted some sub-dirs which had the problems and some other problems possibly solved itself after “revert local changes” - just took some time).
I think it was two cases:
Changed case in dir-names.
Ignored files in the folder.
I got a new error now:
file modified but not rescanned; will try again later
This happened in a renamed folder (lower to upper case), too.