This is the sort of question that keeps NASA scientists up at nights. It's a fundamentally tough problem to tackle, especially with just a rover full of instruments and experiments. You can try to design the experiment such that you can show that it's the presence of external samples which show signs of biological activity and not the parts of the machinery itself (e.g. comparing results with and without an external sample present, comparing different samples, etc.) but even that isn't foolproof.
Keep in mind that for unmanned "life detection" missions a spacecraft would not just be constructed in a clean-room but all of its components (as well as the whole vehicle) would be extensively sterilized (at 112 deg. C for about 30 hours, for example). Additionally, the vehicle would be extensively swabbed throughout assembly to search for any amount of biological contamination.
However, more than likely the focus will not be on an unmanned life detection mission but rather on a sample return mission (which would be optimized to try to find samples containing life) or on a manned mission (which would also likely entail sample return). In either case there would be a considerable amount of research resources available to study any samples of Martian life, should it be found, and bring to bear instruments or tests which would unambiguously show it to be of a different origin to Earth life.
Keep in mind that for unmanned "life detection" missions a spacecraft would not just be constructed in a clean-room but all of its components (as well as the whole vehicle) would be extensively sterilized (at 112 deg. C for about 30 hours, for example). Additionally, the vehicle would be extensively swabbed throughout assembly to search for any amount of biological contamination.
However, more than likely the focus will not be on an unmanned life detection mission but rather on a sample return mission (which would be optimized to try to find samples containing life) or on a manned mission (which would also likely entail sample return). In either case there would be a considerable amount of research resources available to study any samples of Martian life, should it be found, and bring to bear instruments or tests which would unambiguously show it to be of a different origin to Earth life.