Yes, I had the same problem. I watched it (right after playing the battle) and was totally confused. In many cases, units that appeared to be fighting had no animations because they were supposed to be from the same player (even though I know they weren't). So the way it looked in the replay was just two units from the same side standing next to each other. Then one routs, except it didn't really rout it just moved away and not doing the running animation, etc.

Basically the whole thing was FUBARed in just about every way possible.

Since my team lost the battle I recorded, I'm not exactly devastated the replay didn't pan out =).