Mac log files are not necessarily application specific. I've also seen conversion logs write multiple conversions done at different times but in the same location wrote adidtional content to existing conversion logs.
It's hard to decide if this is a bug or a feature. Once you know it's happening, it can actually be useful to know your log is cummulative, but it wasn't expected behvior. I believe the app simply looks for a log file of the correct name in the proper location and uses it if it already exists.
IIRC, the docs on the developer copy of FMS identified the need to move or copy off the 11 log to keep the 12 install from overwriting it. So I think this is expected behavior. Not near my machine at the moment, though, so I can't verify.