This is perfectly normal.
Say you have a train take cargo from point A to point C, where it transfers cargo. Another smaller, or a road vehicle, picks up the cargo at point C, and takes it backwards a short distance to it destination at point B, which accepts that cargo.
Then the first train gets paid for point A to point C, but seeing as the road vehicle takes it CLOSER to the starting point, it gets a negative payment.
Hence the profitability of vehicles isn't that meaningful. The last leg of a journey with multiple transfers often produces nominal negative income for the vehicles, but in reality those vehicles are making you lots of money. In other words, they are "captive" services -- they don't make profit themselves, but are essential for making your mainlines profitable. While the cargo payment model is limited, the idea that local feeder services and minor branch lines are subsidised by the profits of mainlines is actually perfectly realistic.
Does that apply to a passenger bus serivce running between a hotal and a town, though? Or to goods being tranferred to an end-point? That seems to be where the issue is arising, not from anything that's actual on orders to transfer? Or is that now a facet of cargo having a destination/origin? (I'm not sure I played a great deal on 1.5 - I remember the crago destination stuff coming in when I last looked at it), but I don't recall that I was actually getting a loss from passenger services before...?
I didn't think that the estimation from the transfer part could actually go negative.
Edit: I went and watched for a minute or so more. The buses went back and forth and gained some transfer (yellow) and a little bit of income (green) at the respective stops... But not a negative cost this time. (Bizzarrely - unlike the failing goods/material supplies which seem to be costing money when they reach their final destination (on just a single stage from manufacturer to end-of-chain) - in previous years, those particular buses appeared to be doing fine.