I've just managed to move my Interceptor ashore.

Steps to reproduce:

1. Combine land unit and naval unit into a fleet.
2. Move said fleet to your coastal city.
3. Perform an action to garrison your units.   

Save file:

Boat ashore.zip

Right, i think I figured it out. It's basically same bug as this one. After moving land unit to garrison, model for naval unit teleports to semi-random tile (even land), but it's technically still at its place.

These should be reliable steps to repro with AutoSave 681.zip, tested few times at my side, step-by-step guide:

1. Select Boarding Vessel near Byaegol
   
2. Move it to Whiechsul to the coastal tile to the south
   
3. Select Mastermind inside Whiechsul and create an army with it
   
4. Move Mastermind on top of Boarding Vessel to embark it and merge into fleet
   
5. Select Mastermind inside new fleet and garrison it back to the city
   
6. Vessel model glitches and appears few tiles away
   
7. If you select the vessel and try to move it, its true location will be revealed