If it's confusing your classmates, it's serious enough to worry. Maybe a private email expressing some confusion on your part and asking if he actually meant "atom" instead of "element" would do the trick.
I've learned that feigning confusion is not a good way to present corrections. If I say I don't know and ask for clarification, the easiest response is either "I was right the first time" or "It doesn't matter." That ends the conversation, because in saying I didn't know, I gave up any position to argue from.
Speaking as a teacher, I'd want to know if I was making an error or doing anything to confuse my students (although I've colleagues who don't seem to uphold the same standards). Consider sending him a quick and clear email. (Keeping in mind that profs get loads of ridiculous emails from students these days, and the guy doesn't know who you are and where you're coming from.)
I would stay after class and ask him about it directly rather than in email. Don't feign confusion. Say something like, "I've noticed you have said element a couple of times when I think you mean to say atom." and go from there. Direct & Discreet.
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