When using the update feature, many more mods are requested to download than have been updated/added. Specifically I was having issues with this collection where updating 2 revisions tried to redownload like 300 mods and nowhere near that many has been updated.
https://next.nexusmods.com/fallout4/collections/5atq9t

Hi, thank for the feedback, and thank you very much for providing your collection link, almost no one ever give me this precious information for debuging lol.
So, yeah there is an issue with mods that have multiple files like "cVc Dead Wasteland 6" the way I check if there is an update is not correct. I'll try to fix that today or tomorrow.

I just publish an update which should fix your issue (0.9.3)