It happens often enough that NASA has asked FPGA synthesis tool vendors to implement error correction feature on this. Basically, when state machine goes into some error condition/state, the system is reset to a known state.
NASA also needs hardware to operate under extreme conditions. For example, anything that goes into orbit is going to have a significantly increased likelihood of a gamma ray burst (because it's no longer protected by the atmosphere). I'd also imagine that they have a much lower tolerance for faults than your average consumer machine as well (because they're doing things that are much more critically important).