It is more the problem of EMC and less (but still) the problem 'it's been working fine'.
You are right, it's either or both. Some form of common mode voltage equalization is needed for the bus to function. If explicit wire is not used, then there is usually some parasitic route. If it's poor enough, it might not even work at all, not even on lab. If it's good enough, then it might even pass EMC. Then there is large grey area which works usually fine but does not pass EMC.
But really, there should not be separation of "works" and "passes EMC". The only reason EMC regulations exist are for things to work well. So saying something that does not pass EMC "works" is like saying "I can drive under influence because I'm a good driver even when I drink". It is just psychopathic behavior.