Ship docked without being docked

I ran into this glitch yesterday, but the gap was much larger. Almost the full size of a square light armor block.

I approached a floating connector (not surrounded by armor blocks) to dock my ship. The ship gave me the prompt to dock, and after I hit P the ship maneuvered itself to the docking port and says it connected.

However, as you can see, there is a gap between the two connectors, and the ship won't maneuver any closer, no matter how many times I hit C to move the ship down vertically. I can also engage and disengage parking, but the same gap always remains.

Since I am close to base, this isn't a big issue as I can unload manually. But the ship's batteries can't charge from base power, nor can I unload using the inventory screen to drag and drop between grids. (The connectors don't seem to be auto-unloading from the ship to the base either.)

I encountered the second problem again after getting a load of iron. The iron filled the hold to 52% before hitting the full inventory bug. And when I tried to dock, the gap limit was even wider.

The attached video shows me trying to maneuver closer while not docked, and the connector boundaries are not letting me. I parked, and the ship also didn't maneuver any closer nor did the connectors turn green. I also accidentally moved the mouse then maneuvered using the arrow keys in various directions. But the gap didn't get any closer.