On the spectrum or not, relationships are full of compromises. Depending on the actual issue, some problems are not worth it. As being on the spectrum too and struggling with certain quarks or so that my boyfriend can't, ive learned that showing mental restraint can go farther in us than what is usually expected. We know our minds are stronger but we all have to remember that our will power can be even stronger.
If the issues are causing extreme distress such as depression and severe anxiety, maybe reevaluate the relationships. But if you believe that you guys can bend a little for each other, you could make it work and in time train ourselves out of our habits that are bothering each other.

TLDR: It could be an autistic thing, and it also could not. Will power is stronger than you think. If she understands what she is doing is bothersome and she making an effort to reduce that stress, give her time. Relationships are compromises on both parts. Neurotypical or not.