I can't upgrade my ship a second time?

I've upgraded my ship once before, and now that I am maxed out on crew members again I got the license and I went to talk to the penguin guy and he just is trying to sell me hoverbike stuff. Am I doing something wrong? I have 14 upgrade modules

 

Okay so I had to buy the fake license to get the quest to upgrade it.

 

That means that your inventory for weapons/items was full, at the time you got the quest for the upgrade, correct? The issue is that there is a physical license you need to pick up that will disappear instantly once receiving and accepting the quest to upgrade your ship. You most likely missed the card pickup and beamed to a planet, subsequently deleting said necessary object. This could have been avoided by simply picking up the card on the ground.
Do not blame yourself we missed this about 5 times before noticing the card, just check your inventory space next time.

 

Exactly as said above. Once you get the animation on screen saying that you've obtained the license, it will appear just below you as an actual item. You need to pick this up for it to actually work, and once you pick it up it won't appear in your inventory, so don't stress out. Once you've 'picked it up', you can then upgrade your ship.

Note: If you're ever unsure if you didn't pick it up or not, and are worried it may be a bug in the quest, you won't be able to purchase the fake license if you have the legitimate one, so if he doesn't sell anything, you definitely have the license (which isn't in your case, though just saying for future reference. )