I experienced this issue on one of my lines. I have no more information for you, but I will post here if I will have anything more than "it happens sometimes".
EDIT:
I noticed that sometimes trains follow it's schedule in reverse order. I attached screenshots of trains going one after another from Pudstone Station. There was that duplicate departure issue happened.
EDIT2:
Oh and that line had "Mirror schedule" earlier. I resigned from that feature for correct platform choosing. When I noticed that schedule issue, I thought it is a bug, so I deleted line and recreated from scratch. It wasn't help.