Stations that Large ships get stuck in.

[Knucklehead]

Battleships
Battleship Isis, Omicron Minor.

Outposts
Gas Miner Ogashawa, Sigma-19

Stations
Bornholm Depot, Omega-15
Freeport 11, Omicron Delta
Detroit Munitions, NY
Kyoto, Chugoku
Phoenix Shipyards, ???(Vespucci, maybe?)
Mactan Base, Magellan
Mito Shipyard, Tau-63 (Singleplayer mostly)
Nome Base, Kepler
Ruiz Base, Omicron Beta
Rostock Station, Omega-15

Thought I'd fill in the gaps a bit. And here's a few of my own:

Pretty much any Rheinland Battleship
Luxury Liner Hawaii (but not Luxury Liner Shetland...)
Kusari Battleships in Single Player
New Haven Station, Connecticut
Augsburg Orbital Colony
Augsburg Docking Wing (I think, I'm not sure though.)

(All of these use the same basic model)
Friestadt Base, Omega-7
Altona Station, Hamburg
Ingolstadt Base, Munich
West Point Naval Academy, New York

These next few I don't know for certain, but it is possible, since they have a common model with other known problem bases:

Ainu Depot, Hokkaido
Aomori Station, Honshu
South Shields Refinery, Newcastle
Glasgow Outpost, Leeds
Mainz Storage Facility, Frankfurt
Holman Outpost, Tau-31

That's all I can think of right now.

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It's official, I have too few ships now...