Get your taxes done using TurboTax

When preparing your mother's tax return, enter $3,000 as the required RMD, not $12,000.  Upon her death she was no longer required to complete the rest of the RMD.  That responsibility moved to the beneficiaries, which you say that the beneficiaries fulfilled.

The beneficiaries will each indicate in TurboTax when preparing their own tax returns that the amount that they were required to take was only their share actually taken, not the entire amount.