The issue is that ships can be in 2 sectors at once, the docked entities that are not in the same sector as the main ship core have a **chance** to end up docked, in the wrong sector. Causing them to be non physical yet they still are attached to the main ship just in the wrong sector.
We had this issue when trying to dock to something in a different sector than you were originally, that is fixed now yet the stuff mentioned before still happens unfortunately.