I pretty well always have a 4 or 8 AA Eneloop batteries on my Maha charger, and I always have a Canon camera battery on its charger as well. I have done this for years and have never had an issue. Good Li-Ion batteries and good chargers will allow you to do this without any trouble.
Note that John's point about keeping them in the bag rather than on the charger is a good one, but I own many sets of batteries and several batteries for my cameras as well, so I also always have spares in my camera bag too.