It’s not her perception I question; it’s her ability to interpret what she perceives.
Take the outtake from the first Saffron episode when she asks Book to marry her and her brother. This happens because the captain’s just gotten married (thus putting the thought in her head) and, judging correctly that Simon loves her more than he loves anyone, including himself, she thinks marriage is the best way for their relationship to proceed, and seems to think he will agree. If she can’t tell the difference between brotherly love and romantic love, nor understand why Book and Simon will be horrified at the suggestion, she’s not going to be a good judge of anyone’s motives.
I think she read Book correctly insofar as knowing the basic words going through his mind. But she wasn’t competent to interpret those words. Also I suspect that (since the root cause of her craziness was knowledge of what had happened on Miranda) that she was at the time very mixed up and might have mistakenly loathed herself, feeling guilty for what she knew.