I just saw a post with something about bumps when doing MRs... My reply to that one, however, seems more fitting here:

I have been in a few situations where I wanted miles on carrier A and ended up being placed onto carrier B whereas A and B are totally different alliances./

In my experience, you just keep all copies of all things/records, itineraries, boarding cards and tickets and start writing letters.

I was able to get the miles I WOULD HAVE RECEIVED on "A" and then, also write in to get miles for what I DID FLY on "B."

Works every time. I have the ticket for B and just flew it, so it actually should show up especially if you had remembered to give your FF number at the gate before stepping on the plane. But if not, just mail a copy in and ask for credit, without necessarily having to mention the original carrier you were supposed to be on! 99% of the people touching your record once you fly have no concern as to where you were before using that ticket, so you can easily get miles from its use now.

the other airline, however, needs to simply see what you were supposed to fly, and then you just indicate to them how you were told to go fly on airline B. Maybe have a copy of the B ticket for them too, but generally, you should still be able to recoup miles you meant to obtain for a trip they botched up by sending them copies of those tickets as well.

Again, just keep everything and write letters and wait!

In the end, hey, if they do give you miles for both, you deserve them anyway. And if they do not or try to say you cannot do that, just play dumb and pick/take the one that you really wanted most.

good luck!
MM