Yes, these games still happen sometimes. It's an old problem which even Charles had trouble solving. We will address it eventually, but at this time it's pretty low priority.
It sounds a lot like whatever is being used to seed the RNG is being calculated by some attributes of the teams/players and if you were to sim in a test environment the same game ten times back to back, it may well be that it would have the same result over and over. If the random seed is set to incorporate something non-repeatable, like DateTime.Now.Ticks, the duplication in theory should no longer occur.
Of course if it were that easy I imagine it would have already been solved. Usually the things that seem like they'd be the easiest to fix are the hardest to pinpoint.
