Nf calibration has been done before measurement and after calibration i carry out one measurement with noise source connected directly to spectrum analyzer (as during calibration) - so i get 0 dB gain and 0 dB NF, as it should be. So i don't think this is due to wrong calibration. The similar phenomenon i get when i measure NF of microstrip line on PCB - although gain remains constant, for example -2 dB, NF hesitates, sometimes becoming less 0 dB which is physically impossible.
I guess this is connected with reflection waves in case of unmatched load.