1) Was over warehouse to pick up materilas.
2) Entered warehouse.
3) tried to leave warehouse, could not enter ship.
4) Exitted warehouse.
5) Now cannot get to either ship nor warehouse since top left corner of warehouse is "surrounded" by other buildings.
6) Would like to get back into ship.
Message received none, simply no option to get into warehouse I was in nor ship I was in.
There is the Bug Base, if that's what you mean. However, according to one of the programmers you should be able to enter the facility from any side of it; people just commonly park over the top left corner since it's easiest just to re-enter their ship. Are you positive you did everything correctly - you returned to the entry room within the facility and hit the 'Enter' button to re-enter your ship?
If you are unable to re-enter the facility from any direction now, and you are positive it is still assigned to you, you can report it as a bug, being sure to include a full description of what happened as well as the facility ID.