Not *really* a bug - filesystems are "close to the metal", and the lexicographic order used in computers today places 'Z' before 'a'.
To make it worse, mod load order, when no dependencies are specified, depends on lexicographic order -
(well, it *has* to depend on something !).
I'm willing to bet that some mod authors already used capitalization to resolve mod load order issues !
Sadly, it would seem that there aren't any really common best practices for capitalization in file naming - the one that I found that I like the most is to reserve capitals for Important Files, ALL-CAPS for the REALLY IMPORTANT ones.
(Not only that makes them more visible, if you list the files in the case-sensitive order, they would be listed first.)
In Factorio's case that would mean that the only (non-user-created) capitalized files in the mods folder should be Mod-settings.dat and Mod-list.json (currently not capitalized). (Perhaps they even should be ALL-CAPS ?)