It doesn't only happen in uncontrolled or low level airspace.
A week ago in class A airspace I had an airliner refuse clearance from FL360 to FL370 because of "traffic" displayed on TCAS which, in his opinion, was a conflict. I explained to him that he would pass at least 14nM behind the "perceived traffic". He still would not accept the clearance to FL370 until the aircraft no longer appeared on his TCAS display. The closest the two aircraft came to one another was 15.2nM.
I believe that pilots are not being instructed properly as to the limitations of TCAS, especially with respect to azimuth.