There is an MO thread about this:
Basically "our mathematical system" for mathematicians usually (though not always) refers to so-called ZFC set theory. This is an extremely powerful theory that goes far beyond what is needed for everyday mathematics, but it straightforwardly encodes most ordinary mathematical theorems and proofs. Some people do have doubts about its consistency. Maybe some inconsistency in fact could turn up in the far-out technical fingres of the theory. If that invalidates some niche areas of set theory but doesn't affect the more conventional parts of math, then presumably the problem would get fixed up and things would keep going about like before. On the other hand, if the inconsistency went deeper and was harder to escape from, there would be considerable disruption in math.
See Henry Cohn's answer in the MO thread for the longer take that the above paragraph is cribbed from.