Issue reproduced... sorta, it doesn't exactly match the described behavior, but close enough for me to call it the same bug.
I was not able to reproduce it for an unloading station. Attempts to do so resulted in the train unloading as expected, then moving on to the next job or to other waiting bays (if present), also as expected.
Making the loading station a waiting bay, however, resulted in station disablement:

As the cargo-and-waiting station also refused to take a train direct from the depot, I feel like this is intended behavior. Unintended behavior is that once that station had enough cargo in it to request a train... the train still didn't move, and indeed will not move at all until I open an alternate waiting bay for it to navigate to (the waypoint station just to the left of the station in the picture), as it's gotten stuck on an impossible "navigate to waiting bay" job. Recovering the train and rebuilding/configuring the pickup station would probably do the trick, but unnecessary- providing enough waiting bays was enough to get it moving once more. Deleting waiting bay status at the pickup station had no effect on an unstuck train, though a stuck one completely ignored even station rebuilding until the waiting bay was supplied.
I will note that the stuck train did respond to manual "navigate to this piece of track" orders- though it still ignored the waiting job, even after waiting bay status was deleted. It looked like this after I deleted the waiting bay and moved the train:

I would like to note that pausing and unpausing the train removed the "next schedule item invalid" error, but did not cause the train to once more consider the job that's waiting for it. Again, though, the fix was to present an alternate, non-cargo waiting bay.
I am going to guess that all of the waiting bays on your network happen to also be cargo stations, as that would potentially elicit the behavior you described.
Tested on Update 4.1 | v0.8.5 (b598)
I will note that having an alternate, valid, and unoccupied waiting bay, to include the dropoff station, will prevent the train from getting stuck.
For the devs, reproduction of my reproduction:
- Load attached save. Map should be in the pictured position. If not, it's near the bridge.
- Delete the waypoint station as a waiting bay.
- The train will get stuck as soon as it searches for a valid waiting bay.
- Ignore the other trains scurrying around the map, only this test loop is involved.
- To unstuck, re-add the waiting bay.