"Set Position" breaks crafts with robotic parts (or parts attached to robotic parts) if they aren't the craft being teleported that are in the same scene
How to test:
1. Load "Set Position Bug Save.sfs"
2. Look at the crafts beside the runway
2. For the ibeam pocket on the runway change the altitude number to 10 for 'Set Position' (do this before teleporting)
3. Move the ibeam pocket to the Mun
4. Move the ibeam pocket to Kerbin again. (should be back on the runway)
5. Look at the crafts beside the runway
Now you will see that the robotic parts/parts attached to robotic parts have moved permanently
which would break most crafts that this happens to
To make the issue even worse 'Set Positon' to planets further away.
The robotic parts are moving due to the center of the universe being at the new location.
If robotic parts are doing this, there could be other parts that are also doing this?