Była tylko minuta różnicy pomiędzy nimi.

English Translation

There was a minute difference between them.

Is there a difference between między and pomiędzy? I’ve noticed on Clozemaster that only one of them will be accepted as the answer, but I can’t tell if there’s a specific time when you would use one or the other.

No, there is no difference. The exceptions when you have to use między instead of pomiędzy are rare. In general, między is used much more often and in this sentence both are correct and have exactly the same meaning.