This can lead inexperienced mathematicians to conclude that these concepts are related, which in fact they are not.
I would expect the bold part to instead be "which, in fact, are not".
It seems to be the case that the which does not refer to the concepts and it appears to me that there's something omitted. If so, what is omitted here?
I've seen this usage a lot and so I don't doubt about its correctness now and wish to know about its grammar aspects.