Currently, the UploadWizard accepts an upper case file name extension (i.e. JPG), does not change it but neither allows the user to do so (see bug 34703). Therefore, it is possible to upload two files, one ending in .jpg and the other .JPG.
However, elsewhere on Commons, such as in the RenameLink gadget or the tool used by filemovers, .jpg and .JPG are considered the same and the tools won't allow renaming between these two variants, therefore making it impossible to repair consistency if a series of pictures have been uploaded using one case with only one or a few of them accidentally using another case. All these tools seem to share a common "file name sanitization" module, as reported at http://commons.wikimedia.org/wiki/User_talk:Rillke#RenameLink_forces_case_in_file_extension
As evidenced at https://commons.wikimedia.org/wiki/User_talk:Blahma#File:Brno.2C_T.C3.A1bor_15.jpg file movers need to rename files manually if they are requested to change letter case in file extension, such as renaming "foo.JPG" to "foo.jpg".
File names should be treated equally everywhere on Commons, so if file name extensions get "normalized" by file moving tools, the same "sanitization" should be performed in the UploadWizard.