Airlock stuck
Location: Various ships
Cause: Unknown. Cannot reliably reproduce.
The elevator/airlock on bigger ships gets stuck from time to time. It usually happens when landed on stations and returning to the cockpit from the dock (not via shift+d). Either the dock airlock or the cockpit airlock just won't open anymore. Going back to the dock and back to the cockpit level does not fix it. Teleporting to another ship (in another sector), docking, undocking and teleporting back sometimes fixes the issue, but not always. Teleporting to another ship, saving, restarting the game and reloading usually fixes it. Not ship-specific, happened most on my Cerberus Vanguard, but also happened on Cerberus Sentinel and Vulture as well.
Pilot stuck at the helm
Location: Cerberus Vanguard (possibly other ships)
Cause: Unknown. Cannot reliably reproduce.
Sometimes the pilot NPC gets stuck in the pilot seat, they stand on the seat and won't move. They won't fly the ship and I cannot sit in the seat myself either. I can talk to them, but giving them orders does nothing, not even firing them. Teleporting to another sector and back does not fix it. Saving the game and reloading does not fix it. I left the ship at a dock and went to play on another ship, and during that time somewhere it unbroke itself, but I have no idea when or how. This happened twice now. Leaving the affected ship somewhere and playing the game with other ships for a while tends to fix it after a while, but the method is unknown.
Main weapons will not fire (temporary variant)
Location: Cerberus Vanguard (possibly other ships)
Cause: Unknown. Cannot reliably reproduce.
Sometimes the main weapons on the ship ceases to function. Turrets still work. Pressing the fire button either on the mouse or the keyboard does nothing. Targeting/gimbal dots still present. Changing firing groups does not help. This can usually be fixed by pressing Esc until I reach the pause menu, then Esc again to go back to the game, the guns would work again. Could possibly be tied to changing flight modes (shift+space) or ship modes (shift+1,2,3,4).
Main weapons will not fire (permanent variant)
Location: Cerberus Vanguard (possibly other ships)
Cause: Unknown. Cannot reliably reproduce (thankfully).
The main weapons ceased to function on the ship. Turrets still work. Pressing the fire button either on the mouse or the keyboard does nothing. Targeting dots are missing! Changing firing modes or weapon groups does not help. The Esc-trick from the previous bug does not help. Docking and undocking does nothing. Teleporting out of sector and returning does nothing. Saving and reloading does nothing. Quitting the game, restarting and loading back in does not help. Removing/replacing/switching main weapons at EQ dock does not help, the new weapons won't fire either. Seems to be affecting the ship itself permanently. Selling the ship and buying a new one seems to be only solution.
Ship stuck inside central asteroid at PHQ
Location: PHQ
Cause: Design oversight. Reliably reproducable, just stay around or on the station IS.
Ships regularly get stuck inside the large central asteroid. I'm pretty sure it's the command that directs every approaching ship to fly inside the central asteroid before vectoring to the dock. Out-of-sector it's no problem, because no collision, but being on or around the station just screws AI traffic at the PHQ royally. The solution is to leave the sector, either by teleport or a ship, to turn off collision. However this might not be possible under certain circumstances. Right after aquiring the PHQ and building the dock, I landed my Cerberus at the dock. After faffing about on the station for a while, my ship was sent to internal storage because of an approaching trader wanting to dock. However, the ship got stuck inside the asteroid, while still trying to dock, locking down the platform indefinitely. I couldn't recall my ship to the dock because if was "busy", and I had no other vessels I could teleport to, thereby making the game unplayable. Thankfully, I still had a bit of money, I could purchase a small fighter at a wharf I could call to the PHQ, teleport over to it and leave the sector so the trader ship can unf--k itself and I could get my Cerberus back. Please don't make me do this again....
Small station shuttles make navigation/landing a nightmare
Location: Stations
Cause: Those damn things are everywhere!

I don't know who's bright idea was to put AI shuttle traffic inside the friggin docking bay, but f....I'm not happy with you. These annoying little things keep flying under the ship, making it impossible to land with anything bigger than an S class. It's also very annoying when flying around stations trying to scan things, and one of these zits gets tangled into my ship, then the whole ship becomes uncontrollable, it pushes and turns my vessel wildly in every direction until it can unstuck itself from my ships's geometry. This is one of the most annoying things...

These are just most annoying ones right now. I won't even mention the rest, like the traders won't trade, miners won't mine, exploration command not working, NPCs getting stuck, missions bugging out at various stages, AI ships flying into and getting stuck in literally everything, etc. I'll edit the post later if I find more.