What is the meaning of the phrase 'in a league of their own'?

It is an idiom usually meaning that they are separate from the norm. If you said "he's out of my league" you would mean that he was beyond you, perhaps in a higher social position, or you feel unworthy because he is so... amazing, attractive... whatever.

"in a league of their own" doesn't have the same "unworthy" connotation though... and could have a negative connotation. You could look at some people who were outside your own clique or sphere of influence and say that, and mean that they are off by themselves and that is good... much the way we relegate people with mental problems or physical handicaps to separateness or non-inclusion. It isn't always negative, but it could be.

Whatever she/he did is on a another level compare to everyone else to the point where she/he is the only example of the group.

Example- I've never given any score above 88 in my thirty years as a teacher in the UK.This student is in a league of his/her own among all the student I'd taught. He/she deserved a perfect score if not higher.A true genius.

PS:Its possible to use it sarcastically as a bad example,but no one have done so that much.Afterall this is positive connotation.