So, I am not sure the Units tokens are a problem. I was landing on a number of my Frigates lately and I wondered if they may be where the tokens are coming from. At any rate, when I started my game, I found my Freighter full of them.
In your absence, Gek crew members are running a clandestine betting syndicate based on races held in your cargo hold.
That’s where the unexplained credits are coming from.
You should deal with this firmly, as the system authorities consider illegal gambling to be a major offence, and will hold you, as the owner, responsible.
What you are seeing coming through the floor, is the top of the hangar stairways that leads towards the entry of the freighter. No idea why it is misplaced, as this should be lower to not be visible.
There are quite a few issues with the freighter since Beyond. I really hope they will get to fixing these.
My ships had all moved as well. I also still see daylight coming through the roof. I have no second floor. At least running is not throwing me into space, 
I found the same racetrack last night! I thought, “has this always been here? 
”
And I have no idea what to do with these Get Units, but they’re clogging up all my ship storage!
Sell them! 
Yep they’re redeemable at a trade terminal.
I have those tramlines on all my Atlas Rises era freighters but not the one I started after Beyond.
