First, the ultimate workaround is to NEVER use spaces in savegame/spaceship names. This solves:
1. Most savefile gltiches (duplicates with 0byte size, corrupt saves, crashes on overwrite, etc)
2. Non deletable ships in starport choosing queue (which dont show up on ship design)
3. Duplicate names on ship designs (ie, multiple ships with same name appeared on the list, even though they are not in the ship design page)
4. Crashes when overwriting a ship's name.
5. Probably a few other minor problems...
Note: interestingly enough, if you save a ship's name as "Devastator MK1" and then try to save another ship with the same name only without the space (DevastatorMK1) it will ask if you want to overwrite and try to overwrite the one with the space. This HAS a chance of crashing your game, making 0byte duplicates of all your saves, and corrupting your last save aswell as making the Devastator MK1 design a permananet member of your construction list... I will STRONGLT recommend DELETING all ships with a space in their name... and THEN recreating them...If you need, save them under a different name without overwriting (to keep design) and then delete the one with the space, and then rename them again.
Specific workarounds:
Problem: Ships cannot be stacked properly, creating empty fleets or incomplete fleets.
Solution: Save the game, exit, load save...
Problem: A quicksave you just did doesn't show up...
Solution: From my experience it is always there, and exiting to main menu causes it to appear. However you might want not to risk it and go ahead and make a second save just in case.
If you have more workarounds, please post them here and I will add them.