[Original title: "Change the file extension of a file to the most commonly used extension in the time of uploading (like .JPG to .jpg for images, .ogg to .oga for audios, .ogg to ogv for videos)"]
See my comment on https://commons.wikimedia.org/wiki/Commons:Help_desk#File_format_changes_automatically_while_moving_Audio_Files (https://commons.wikimedia.org/w/index.php?title=Commons:Help_desk&oldid=205417112#File_format_changes_automatically_while_moving_Audio_Files, permalink):
If file extensions (not format) changes while they are moved, then they should have changed on the time of uploading. This change of file extensions create some problems, like group of files not in harmony (which is caused by one or more files having different file extensions), forcing a filemover to move a lot of files in the group to be in harmony instead of moving just few. I will be filing a task in Phabricator about this. ★ Poké95 12:31, 2 September 2016 (UTC)