At present there are some correlator problems which produce bad values in the lag data. High atmospheric phase noise, or instrumental problems, result in loss of correlation, or wrong phases, and should be flagged. Amplitudes which are too high or too low can be easily flagged for all the data. You will need to do this separately for the calibrator and the source using estimates of the expected source flux density and the instrumental noise level. You may wish to be more or less conservative, but in any case the process is best iterated between inspections of the data and image quality.
Phases are the best indicator of correlation.
If the calibrator phase is very scattered, or shows phase jumps, then these time intervals are best flagged bad for both calibrator and source data. This takes more detailed uv data selection in uvflag. At present the on-line passband calibration is quite poor and the instrumental passband is both time and baseline dependent. The gains of the spectral windows are not completely removed by the on-line passband calibration. Accordingly, it is best to calibrate the passband for each baseline and spectral window.