Well, that really depends on the source of the failure. Do you know why it fails? If so, have you tried to isolate that fault so that it doesn't trip up the unit test?
Personally, I'd say that if it's genuinely 1 in a million and you know why it's happening, then add a comment to that effect and don't worry about it. It's not likely to bother people significantly in a continuous build, after all. Of course, if it's really one in ten, or something like that, that's a very different matter.
I would at least try to remove the source of incorrectness though. For one thing, it suggests your test isn't repeatable. Sometimes that's okay - there are some sources of randomness which are very difficult to extract out - but I would try not to do it. If you've tried and reached a block, then the pragmatic thing to do is document it and move on, IMO.