How to deal with the (hidden) feedback from research supervisor?

Actively ask for actual feedback. Of course, you need to be prepared for any feedback that is to come.

I am reading things into this... but I suspect you are reading feedback into their facial expressions and body language because you in fact need more feedback.

I had a supervisor who made an "upset face" whenever I talked to her, especially during my presentations.

I told her my observation and asked her (politely) whether my interpretation was correct.

You seem to be frowning. Is it because you disagree with what I am saying?

It turned out her "upset face" was actually her "focused face".

No, I'm just a little tired and trying to concentrate. Please go on, it's interesting.

In short, "hidden feedback" is an interpretation you're making. It may or may not be true, so make sure to double-check.

A short supplement to skymningen's answer: I have made the experience that when actively asking for feedback it helps to emphasize that you welcome criticism. That way an "Everything is ok." answer is less likely.