Can you research UFO Theory?
I can, yes. Maybe this is it, as I haven't touched most of the research topics; it takes FOREVER to complete these and I'm running a crowded base with two labs and a full complement of twenty scientists to men their stations. As for the Yard and its distance to my research center, it's pretty damn close, about two inches away.
When I click the Yard, there's no mention to aliencraft on transfer or of what is already stowed in, but when I capture a NEW vessel and choose to keep it, the dialog box tells me some of my Yard's been occupied (by the other UFOs I kept, I believe).
This game is fantastic and I can see it evolved much through the years and hard work of volunteers, so I'm grateful for it. What is missing (or in need of a fix) is trivial in comparison to what's been done. I can live with the few bugs I've encountered, knowing that these too will be gone before long; more weapon choices for snipers, portable/throwable fluorescent lights, better AI, et cetera are all great ideas and will come up in a future version... eventually.