If it counts, I encountered a Java file that, unbeknownst to me at the time, was duplicated across two different places. The project was essentially abandoned for years, and the file was one that didn't change much so I left it alone for a year or so.

Eventually I had to add a method to it. Compiled just fine, runtime through a no such method error. Turned out Eclipse was using one, but when Maven did its build it used the old duplicate I didn't know existed.

Took me a while to find that one!