In my personal experience I have found that every single time I speculate or read too much into an action or text or behavior I have been wrong. We're all in a state of over thinking because we don't have much to go on but in my opinion, it does some of us a huge disservice.
I think it's more important to take things at face value and gauge our reaction accordingly in the moment. Instead, we over think and mind read and speculate when we're alone and wondering what the heck is going on and that does serious damage in the moment.
About the crayon thing, did you at least communicate with her at hand off that you didn't have the required paraphernalia to complete his homework this time but you will have crayons on-hand at their next visit (it's a stop at Target, $1.99)? This prevents resentment and anger on her end (not that she'd have a good reason but that's not the point) which in turn puts you in a good light. Can't hurt, might help.