This is happening to me now in 2.5. The F1 window even said "fell through the world" twice.
It started that I made a chemistry station on a workstation, then added something else to the station as well (there was nothing in the production queue). Later after picking everything up from multiple stations (I have 3 atm), I noticed I did not receive a chemistry station.
To Resolve -- I exited the world and reloaded it, checked the workstation again (empty), then attempted to spawn the chemistry station with "giveself chemistryStation" while standing in my stilt building, I suspect it went through the floor and I didn't notice. I went down and out onto the ground, then tried it 3 times real quick --> that produced 2 "fell through the world" messages. I figured it was spawning just under the floor for some reason, so I jumped up on 4 frames (1 might have worked) and stood at edge, then "giveself chemistryStation" .. it spawned and fell on the ground. I now have my chemistry station.
Interesting further note -- after all of this, then I found a chemistry station on the work station and 1 other object I had made. I could have sworn the production queues were blank. Maybe they were showing blank, but then completed while I was doing other things.
(so 3 different potential bugs, and 1 potential user error... =) )
