If you ran those scripts while subreddits were dark, the script can’t see those comments you made in those particular subs, (they’re hidden along with the sub) and can’t delete them. Then later when the sub comes back to public mode, your comments will appear as well. So comments you thought you wiped were simply hiding.
Just to add, also check the other sections on your comments when deleting (eg: hot/controversial) because sometimes those ones get missed by the scripts as well.
Not to say that’s the only thing going on… wouldn’t surprise me if they are bringing back some stuff considering their history of shenannigans.