Although .mov files are just videos and non-executable, MediaWiki still consider them as malicious. See https://commonsarchive.wmflabs.org/wiki/File:Combined_cycle_animation.mov for example.
Not much of an issue, but it would be better if the misleading warning would be removed.
Commons don't allow .mov files, so Commons should not be involved here.
Just to be clear, you mean the warning that says "This file type may contain malicious code. By executing it, your system may be compromised." (mediawarning)?