I'm not sure how to share a save.
I will say that I encountered this problem while in a sandbox mode game rather than a freeplay, if it matters. But it shouldn't matter, right?
But there is definitely something wrong with the depots.
Test 1:
Set up a supply station, a demand station, and a depot. Place the train on the track. Send it to the depot.
LTN builds a station and sends the train to the supply. Then to the demand. Then to the depot but it never stops, so just keeps going from supply to demand to depot.
Test 2:
Manually add a "wait 10 seconds" condition to the depot stop. Send the train to the depot. But ... every time the 10 seconds wait time passes, it recycles and starts waiting another 10 seconds. Again and again. Instead of the green bar just filling up in the schedule UI, it fills, blanks, fills again, blanks, etc. I can't remember for sure, but I don't think that previous versions did that.
Remove the requested materials from the demanding station. LTN builds a schedule and starts to execute it. But first it waits until the 10 second bar is filled. Then it goes to supply and then demand. When it returns to the depot, the rest of the schedule is blanked out, but the depot schedule is not reset. The 10 second wait is still there, and it does the same cycling behavior.
Test 3:
Changed the settings so that schedule is reset after delivery. Removed requested items.
A new schedule was built and the train (after waiting for the depot timer bar to fill up) went to the supply station. Then to the demand station. As soon as it pulled out of the demand station the supply and demand was deleted from the schedule. The depot schedule was unchanged (including the manual wait time I had specified). When it got to the depot nothing changed from before -- it stopped there and then began cycling the wait time bar.
Test 4:
I blanked out the schedule and sent the train out of the depot to a temporary stop. Then I made sure the "schedule reset at delivery" was turned on. Then I sent the train to the depot. No wait time was generated in the schedule, but it did stop at the depot because there was nowhere else it wanted to go.
Once again I removed the items from the requesting station. A new schedule was created and the train left instantly. It brought the items to the requesting station and then the schedule blanked out except for depot (with no wait time). It went to the depot and sat there, since that was the only thing on its schedule.