We have run into a situation where we have the same collection on many shards, but the definition of one of our indexes in this collection varies from shard to shard. In one shard it is sparse and in the other it is not.
While this was our fault, this state blocks these collections from being balanced, as the balancer throws this error:
"failed to create index before migrating data. error: IndexOptionsConflict: Index with name: eIds.tId_1_eIds.v_-1 already exists with different options"

We are trying to remedy this by just dropping the index entirely and creating the index in the background (as a side note, why on earth do indexes create in the foreground by default).
This does work, however we have to repair something like 100 collections, and twice now within the first 5 drops, one of these drop indexes will completely lock up our system.

I will try to reproduce this locally without the full production environment in an effort to see if this problem is tied to the indexes not matching between shards.