Alright! New Information!
I noticed that the system still doesn't like landfill, so I kept an eye on it when it got stuck. New discovery, If there is a fish, it gets stuck. Once I noticed it, I tested it. I placed a small square of landfill over a patch of water with 2 fish. It proceeded according to plan, until it got to the fish. then stopped.
Need to remove the fish first, then place landfill, then structures.