Which files are you referring to? Are you saying this is applicable to all files under, say, your system/ directory? Or are you referring to files that EE generates like the system/cache/ files or files uploaded through the File Upload Utility?
If the first case, then I have no idea what could cause that. EE doesn’t modify its own core files, so I don’t think that’s anything that EE could have done. I’d contact your Host/server admin about it to discuss how it could have happened as well as to have them correct the User and Group settings.
If the latter, then it may have to do with the user under which PHP runs (just in general; totally apart from EE). When files are generated by an EE program, they take the User/Group file permission information from the user under which PHP itself is running.