My favorite is the era-dependent strength of ALL embarked units (hadn't been corrected up to the version that I'm currently playing, which is out-of-the-box G&K):
It was late game, the majority of my military units had things to be doing, and a nearby offshore barb encampment kept irritating me with galleys and triremes. The most sensible method of defeating them, since my tiles were pretty much all improved, was to embark my WORKERS. So naval units, designed to pick off embarked land units w/o an escort, weren't just countered by unescorted embarked units, they were defeated by NON-MILITARY, unescorted land units.
"If you keep sending your cats, we'll be forced to sick our mice on 'em!"
I think it was in Vanilla where embarked units were instantly destroyed by naval units, they must have changed it because the AI was particularly bad at tactical movement of embarked units; a single Trireme could 15 Riflemen and they would just keep sending them.