Inertial dampeners cant cope with multiple grids/subgrids.
Any craft with the capacity to keep itself in place has the following issue:
Attaching a subgrid via rotor or piston, or any grid via landing gear or connector will cause the main craft to slowly sink or tilt until it falls from the sky.
I have linked a blueprint that shows this with a rotor at the bottom of the post. If you sit the camera very close to the arm on the rotor you can see it slowly dropping. Eventually the craft will tilt too much and fall. You can replace the rotor with a piston with a few blocks on or a landing gear with blocks on. The problem is the same. Attaching a landing gear to one side of the craft can sometimes cause it to even tilt in the wrong direction.
I have also observed the craft continue to tilt slowly even after deleting the rotor or piston. Which may be another issue entirely.
I used a lot of words but essentially: Any craft with rotors or pistons or docking craft cannot remain in a gravity field without eventually crashing.