Cat owners, I need advice.

This is my Ebony, my precious

So right now she has fleas real bad, thanks to my husbands dog. So I've been keeping her in a crate over night so she doesn't bring fleas in the bedroom (Have a no animals in bedroom rule right now). Well I've been feeding her in her crate and recently she's been pooping in her food bowl. Like she wasn't originally doing this, why is it happening now?

I feel like I need to add to this. She doesn't hate the crate, she doesn't meow until morning, or fight me while I put her in. And honestly she only poops when I put food in there with her....