Something happening between them once before of a sexual nature doesn't necessarily change Bella's protective "older sister" behaviour towards Jill, as it depends on the nature of what happened. A likely scenario for me would be that it was a one-time only make-out session brought about by feelings of loneliness and depression in both of them, mixed with alcohol to lower the inhibitions. Bella going through her issues with James and Jill feeling hurt by another failed date (possibly the one with Rusty), could certainly put them both in a mindset of wanting intimate closeness with someone to ease the pain, then you throw in a few bottles of wine to drown the sorrows, and there you have it.
Bella can still feel protective and want to look out for her like an older sister after this because it was a one-time mistake that doesn't change how she feels about Jill or Jill feels about her. In fact, it could make Bella even more protective of Jill because she feels as though she abused her trust and took advantage of her, hence why she'd be more determined to look out for her in order to assuage her own guilty conscience.
Whatever happened between them, Jill is aware of it and if it were the "sleep humping" thing, then that would mean Jill is aware and it calls into question why she would let the MC sleep in her bed with her in Ep 3 if she knows this is something she does. Given how Jill's character is, she would surely have been very reticent to allow him in to her bed since this might happen, and the fact that she does would seem to suggest that she is unaware. Also, just because she did it that one time does not necessarily mean it is part of her regular behaviour.
It would also seem to have something to do with James since after the argument, Bella pushing of the 2 of them to the floor in what appears to frustration. So what happened between perhaps relates to her problem with James, and something that seems like it would have such an impact is if she and Jill had a moment intimacy that James witnessed.
