> i.e. that our equations just confirmed what we observed

No, no, it's the opposite, and it's key! What we had been observing kept matching what the equations gave us "so far". Without cherry-picking, or refusing to see the cases where the model doesn't apply (consciously or not), which would have been confirmation bias.

We did, in fact, question the model as soon as we noticed it didn't apply.

Confirmation bias implies "cognitive blinkers", I don't think this happened in this Newton vs Einstein stuff.

But I agree the confirmation bias risk is not very far away. It's an issue in the general population, it's also likely a big issue in research.

Don't we start the equations after observing a phenomenon? It wouldn't make sense to try to explain something before observing it..

For example, after observing black holes we understood that Newton's was not enough to explain them. Thus we had to find another theory that explained our observations. Now with quantum computing we know that Einstein's theory is insufficient, too (not very knowledgeable on quantum physics myself, though)