Although there was an ATC failure, Mr. Nielsen tried his damndest to cope as best he could.
The Bashkirian Airlines crew had all received TCAS training and the TCAS operating manual used for their course was quite specific concerning RAs and contradictory ATC clearances - even though the Tu-154 manual was rather less so. There was a 'seat swap' in progress as the co-pilot got back into his seat after the first TA - he made the point several times that the subsequent RA was very specifically ordering a climb......
Read the report in full, I would suggest.