We had to fill out an entire HACCP and friends plan for this! While I won't go over everything that could possibly go wrong, I'll hit some of the highlights.

1. The wrong micro-organisms could grow within the system. This would have certain "cues" that would show up in sensor data. If this happens, the entire unit can be emptied out, the substrate can be dried out, and the frame can be disassembled and disinfected.
2. Speaking of sensor data, while the system only needs a few sensors to operate, we have multiple redundant sensors installed in the case that one fails. If they somehow all go berserk and fail, the user can easily swap in another one.
3. We have humidity stabilizers that can pop with mishandling. It's bad for the plants (though not for humans) if these get punctured and leak out into into the substrate. We've segmented them off, have drip trays in case of punctures, and instructions on how to change them out. To clarify what I mean about the humidity stabilizers being not harmful for humans: you can literally drink the gel inside them. It wouldn't be tasty, and it'll give you a major stomach ache, but it's 100% food ingredients in there.
4. Finally, let's say something unforeseen goes terribly, terribly wrong in one of the units, and it can't be fixed - maybe some sort of weird Martian bacteria gets into it or the electronics (and all the backups and all the replacements) on a specific unit mysteriously fail in some way that can't be fixed. Because the system is made of several units, the others are all separate and unaffected by the issue. In the case of a weird bacterial infection, the infected unit can also be sealed. The seal would act as a quarantine in this case!

There's a lot more on our documents to NASA, but I didn't want to make this comment too long!