I get where you’re coming from. Especially at the beginning I run into this problem a lot. Since back then I knew the kanji / vocabs already I had some of them internalized pretty well. So when I typed onna for 女 I was pretty confused why on earth this should be wrong 
Maybe it is especially since WK is doing a great job differentiating radical / kanji / vocab by distinct colors. This sometimes can trick my brain into “i got it, its a […] that is requested”.
But part of the whole idea behind how the app is structured is to not get your brain into some kind of auto-mode. So I always (try to) remind myself to double check before hitting enter… or live with the results.
Apart from this, I totally agree with what many others mentioned already. After using WK on a regular basis I figured out strategies to (somehow) pay more attention whether it is reading or meaning that is requested. Just be patient with yourself 
I don’t think the main app will be (nor should be) changed. But maybe you can ask in the scripts section if someone would like to help you out with a user script doing some additional color changes.