Noticed two bugs that might be related (and also may have already been reported.)
When changing the control mapping, pressing the button you want to assign also registers as using that control; specifically, remapping the use button caused the remap option to be immediately reselected, then re-remapped, causing the button to briefly oscillate between the two states. This would sometimes end with the button being properly remapped, but not most of the time. (This most likely happens with all of the controls, but I only remapped use and back, with back predictably backing me out of the menu as I made the change.)
The other bug has to do with missions getting canceled. At the beginning of my second or third delivery mission, as I was moving the first half of the crates onto my ship, I was informed that the mission had been canceled due to missing cargo. I accepted another mission and began loading new crates and unloading old ones. This seemed to be going fine at first, but on one of my last two loads, the same missing cargo alert popped up. Both times this happened, I had picked up a crate immediately upon re-entering the ship due to either continuing to hold down the use key after activating the lift, or accidentally retapping it. Due to this, I think the game lost track of the crate because I was holding it when the ship loaded in, so it didn't detect it where it thought it should be.
These problems seem related to me, because I think that a touch of input delay on certain actions would at least partially solve both issues.