The Havoc civilian bomber model's hitbox is slightly too big, and I get caught on stations at least half the time I attempt to dock. This happens more on battleships, maybe 75% because I'm forced to dock with the fighter bay doors. When it happens I need to alt+f4 in space to un-stick my ship because I'm trapped in the docking animation forever.
Here's a pic of my a few minutes ago stuck on Battleship Ottawa.
Screen #1 Screen #2 - Happened trying to dock with Ottawa just after I posted this.
I'll update this post when it happens again, to get more screens of the kinds of places I get stuck. Also this is only when I auto-dock on stations where I miss the insta-dock point.
Even though the ship's hitbox collides with the opening I've never been stuck before. Sometimes you just have to wait a moment for it to realign and dock correctly.
If that doesn't help, just quickdock. The quickdock point on most Liberty Battleships is in close proximity to the bridge.