I use Sonarr, but it does mess up sometimes for shows even when you mark it as an anime to use absolute numbering. It most often happens with older shows that have lots of OVAs that are sometimes listed as episodes and sometimes listed as specials, depending on the database. So, if you are having Sonarr manage your downloads, then it can grab the wrong episode if it’s database (I think TVDB) and the release (usually using MAL numbering) disagree.