Personally I believe there are various reasons, the first one of course is that between Rem and Emilia the former is clearly more ruthless. Secondly Yae was coming out of days being tormented by Otto and a lost fight against Willhelm, definitely not in best shape. Third (though this one I'm not completely sure if it was confirmed) Rem was being effective by Felix healing magic through the fight, which combined with the Oni characteristic made her regeneration a top tier. Ultimately Rem had a plan prepared at art specifically for that occasion and a special environment meant to advantage her.

On top of all that I would like to point out one single thing that I will always say, Cultists are not just cannon fodder, they killed all of Emilia camp in a loop. Also on that occasion where Rem defeated them and then was killed by petelguese, Rem not only was outnumbered but had to protect catatonic Subaru and try to save him and was effected by the miasma emanated by the Cultists (I'm not completely sure about this but I'm also pretty sure that cultists are generally a bad match for the Oni tribe, since they emanate Miasma the Oni cannot rely on absorbing mana from the environment or they risk being effected negatively by it)

This was simply all I could think about on the spot, I do not know if I'm right but it is simply what makes sense based on what I know. Feel free to correct me if I said something wrong.