First, I want to comment on your statement that saying that electrons "orbit" the nucleus is "wrong" ... it may be wrong in some respects, but it is a useful simplification. It is a good first step into some area of interest, the details of which can later be revised.
And notice that with math, notions of 'right' vs 'wrong' are even harder to pin down. Is Euclidian geometry 'wrong' and non-Euclidian geometry 'right'? No, both are simply different worlds that we can study in isolation. And as far as their application to the real world goes, both turn out to have their uses.
Still, something analogous to the electrons "orbiting" the nucleus could be set theory: Naive set theory assumes that there is something like a Universal Set: a set of all things. Now, this is certainly an intuitive and helpful concept, and you can use it to prove all kinds of elementary results in set theory. However, it turns out that there is no Universal Set: that the idea of there being a Universal Set leads to a logical contradiction. So, this is something that more advanced students of set theory will be taught, and they will learn a more sophisticated axiomatization of set theory that hopefully avoids any such contradictions. And note I say 'hopefully', because we actually don't know if modern set theory is consistent: so maybe the large bulk of mathematics that can be based on it is 'wrong'!
The point is: beginning students are unlikely to ever hit upon the contradiction hidden in naive set theory. So, naive set theory is still very useful and perfectly ok to use in that context. ... it is certainly a lot easier as an introduction to set theory.
So, the answer to your question "Are there things being taught wrong" is yes and no: Yes, in naive set theory we teach something that is "wrong", but I would not say that it is 'wrong' to teach this 'wrong' thing. Sometimes to teach well, you have to initially teach things that are 'wrong' ... and from a pedagogical point of view, it is sometimes 'wrong' to initially teach things that are 'exactly right'. The truth can just be too much too handle for beginners.
Indeed, we often take this staggered approach to the very notions of right or wrong, . First, we are taught that there is a clear 'right' and 'wrong' ... and only later (when we hit secondary education) do we learn that things aren't as black and white as we had always thought.