It has been a couple of years, but I was working on a rather complex RoR application and trying to fix a bug, where I had serious trouble understanding the underlying behavior. I went through the library docs, gave our code multiple screenings and was just stumped. - Turns out, we were monkey-patching an issue that was a also resolved a couple of years before, in a slightly different way than the library authors, and this was leading to very subtle issues down the line.

Now of course, we should have long removed the monkey-patch, or properly documented it somewhere, or I should have been more knowledgeable about Ruby and known that monkey-patching was a thing, but there's a reason why it is a pretty frowned upon practice.