I can't find a way to reliably reproduce this issue, however one current example is at Aldinghall Junction 3389,811 on the bridgewater-brunel server. At some point (I believe well over 2 game-years ago) a disruption on a particular line caused waiting times for that line to rise drastically, and many of these times have not changed since despite a frequency upgrade. The waiting time for trains to most stations on the line is 5:18 given the frequency of 10:39. However there are major outliers including Nutingwest (4:10:54 hours), Bloxingpike (4:05:30), and Staningsea Junction (34:30 minutes) and a few others on 7:54, which was the original waiting time before the disruption and frequency upgrade.
Travel times generally seem correct, and I have ruled out overcrowding as a factor as the trains are usually well below seated capacity.