This is an issue related to have docks on your design. Ship size does not matter as this even occurs on the smallest of examples.
If you **deconstruct** or **unload a design** of a ship that has docks on it, not everything of that ship gets wiped properly after it is finished deconstructing. I believe the shipyard will still think the docks are there, giving a false positive for designs you're trying to load that have their own docks overlapping with them.
It should load the design still most of the time, but you will often fail first and then succeed on the 2nd attempt. I'm not sure if that's because a failure to load wipes the bad stuff already, or that it is just a coincidence of my test setup. Should be absolutely fine if you try to load a design that has no docks at all though.
The issue itself can be worked around by unloading/loading the sector again.
You can also construct/deconstruct a tiny ship without docks to wipe the old data and reset it back to a normal state. Loading/unloading the design multiple times should work too but might depend on ship size and dock count.