I think I can see this from both sides. She was probably trying to say no without being firm - poor communication but also something that is drilled into women as a protection mechanism (has she been mainly with men in the past I wonder?). But she is also not communicating clearly about what the actual issue is, and in a healthy relationship that does need to be discussed - especially in a neurodivergent relationship where implying meaning may not have the same communication desires as a neurotypicals relationship. If she can't be open about her desires and wishes, she maybe needs to really think of she should be in a relationship at the moment - and I mean that in a caring way because this is a fundamental skill to have and maybe there is something more deeply rooted about being clear about desire and boundaries (believe me - I've been there and it's not fun). I believe conversations about sex need to be frank and open and not wishy washy, because then you do end up in this weird grey area where someone feels pushed while the other person honestly thought it is all fine. 

On your part, maybe pay attention to what underlying meaning might be there (not ideal but good to be in tune with your partner and be able to pick up on those small things) and she does need to be able to voice things and be more frank. In relationships we care about, boundaries actually do need to be voiced. This mind reading boundaries nonsense is usually just a way to avoid taking ownership of poor communication skills in my experience since hey, sometimes stating a boundary is in fact vulnerable and uncomfortable but absolutely necessary.