What is the reason for it? Unlike windows, some Linux servers may consider files in different case to be different and do not overwrite them. So you'll have e.g. controllers for both old and new K2 version.
In K2 version 2.5 corresponding files are lowercase.
If you have such an issue, just delete older files.
Otherwise I suppose that in some cases the possibility of referring extensions to old version files exists and may cause issues.