I think a more plausible scenario for the atomic theory being wrong would be that the scientific community -- and possibly the scientific method -- is somehow fundamentally borked up.

Humans have come up with -- and become strongly confident in -- vast, highly detailed, completely nowhere-remotely-near-true theories before, and it's pretty hard to tell from the inside whether you're the one who won the epistemic lottery. They all think they have excellent reasons for believing they're right.