Not a full answer, but I would expect most of this kind of debate to be in more informal channels rather than journals (as in LiorSuchoy’s answer).
Einstein, for example, was a prolific letter writer, and corresponded with many of the great physicists and mathematicians of the day, e.g. Born, Cartan and Schrödinger (from a quick google it looks like the Schrödinger letters are still not published as a collection, so I haven’t linked them).
I read the Cartan letters, some time ago. I don’t have access to a copy now, but IIRC they get much more into picking at disagreements/clearing up confusions than anything you’d find in journals. For example, I opened up the Google Books preview, and immediately found the following from Einstein (on page 13):
I am sending to you my articles on the subject, published so far by the Academy. The second, on the approximate field equations, suffers, however, from the drawback that, with the choice made there for the Hamiltonian, a spherically symmetric electric field is impossible...
Then as well as letters, there’d be conversations at conferences, gossip over lunch and in department common rooms, question sessions after lectures. This stuff is mostly lost, though, whereas the letters can still be read now, so that’s where I’d look.
All of this still goes on between researchers now, of course, and that’s still how news travels in individual research areas. If you want to know what’s wrong with published papers you’re much better off talking people in that field than trying to find retractions in the published literature. But academia was so much smaller then that informal networks of correspondence might plausibly cover large areas of science rather than a small research speciality.
Ooh, I’d forgotten about that test, and how the beer version was much easier—that would be another good one to read up on.