I am not sure at which point we can prohibit this. Because I assume we wouldn't want to prevent someone from entering two references, starting both with the same snaks and only then adding the differentiating snaks.

I think it should be prevented in any case. More precisely, I think we should prevent adding exactly equal references and also adding references which present the same parts in a different order, and afterwards we should send a cleaning-bot.

I add an example:

1. I added one reference
2. then I added the same reference, only changing the order of its parts: it worked (https://www.wikidata.org/w/index.php?title=Q369129&diff=1320370815&oldid=1320370672)
3. then I added the same reference, exactly equal to its first configuration: it worked (https://www.wikidata.org/w/index.php?title=Q369129&diff=1320370908&oldid=1320370815)

Both the second and the third case should not work.