Yes, "do not pair" lists do exist. They were brought in as one of the responses to the crash of Northwest Airlink Flight 5719. The accident was basically a CFIT (Controlled Flight Into Terrain) attributable to pilot error, but the attitude of the captain was cited as a major contributory factor. He harassed, brow-beat and bullied his junior first officer to such an extent that he became timid and ceased offering advice or opinion, in violation of accepted CRM rules that state that cockpit crews have to operate as a team.
After the crash it became acknowledged that personality clashes can have a very detrimental effect on CRM, so if there are certain flight crew who have trouble cooperating they can request to not be paired up. The airline is then obliged to try to accommodate those requests not to be paired up. The safe operation of an aircraft requires the crew to operate as a team.
If you don't trust Wikipedia, the National Geographic TV show Air Crash Investigation also covered this flight and its consequences.
The full NTSB report is available online, and cites a breakdown in communication leading to loss of situational awareness as a major factor in the crash (PDF)
The National Transportation Safety Board determines that the probable
causes of this accident were the captain's actions that led to a
breakdown in crew coordination and the loss of altitude awareness by
the flight crew during an unstabilized approach in night instrument
meteorological conditions. Contributing to the accident were: The
failure of the company management to adequately address the previously
identified deficiencies in airmanship and crew resource management of
the captain; the failure of the company to identify and correct a
widespread, unapproved practice during instrument approach procedures;
and the Federal Aviation Administration's inadequate surveillance and
oversight of the air carrier.
It should be noted that the NTSB report does not explicitly recommend "do not pair" lists as a remedy against future occurrences, it mostly focuses on improving pilot training, and also on improved illumination on the wings to help pilots spot icing. The Air Crash Investigation episode does say that the report led to airlines adopting do not pair lists as a way of avoiding future incidents like this one.