Euhyperamoeba biospherica
According to december's Wired, one of the lessons from Biosphere 2 was he absence of natural predators made it possible to an amoeba, the "Euhyperamoeba biospherica" to thrive....It wasn't dangerous,but it happened.
If a crew goes to Mars with a closed ecological system, it's perhaps not Mars microbes that might be the most problematic, but stowaways from Earth, contaminting the crew and not Mars.
Raoul