This is my current location : http://img76.imageshack.us/img76/5587/syn1vk.gif . I'm in the ship, and I'm trying to get into the facility. I am the manager and operator of said facility, and am on the crewlist.
If I move my ship one square to the left, and leave the ship, I can enter the facility from the ground. But with my ship in the position show in that picture, I can't enter the facility - it tells me that "There is no facility, ship, space station, or vehicle where you may enter." Since I need to move materials from this facility to this ship, this is a bit of a problem - the ship has to be in that position to move the things, but I can't leave the ship, and I can't enter the facility directly. I've spoken with Syn, and I'm told that this is a bug of some sort.
Oddly enough, I'm having exactly the same problem, but I'm onboard a different ship, and trying to board a station. I'm in the exit room, the ship is at the right location, and I'm on the crewlist, but I'm told that there is nowhere that I can board. And someone who is on the station is unable to get out.
Earlier this morning, I considered trying to dock my ship aboard the station - of course, there was no "dock" option available, but then, there shouldn't have been, since my ship wasn't on the approved ship list. A few hours after that, however, I was made commander of the station, and suddenly I did have a "dock" option in the travel menu - but when I click on the dock button, it tells me that there's no where that I can dock.
Mack was having this same problem when I asked him to pick up some materials for me. The facility was assigned to him and he was at the right position and all that, but it said there was no station, facility, etc. to enter. I even tried opening it to all to see if he could access it then, but no such luck. Sigh.
I've had the same problem with my mines, as have some of my employees. For now, I just go outside and then enter from there, even if it takes much longer and I can't seem to be able to move materials into my ship when it is merely next to the mine and not above it.