Well, those ducts don't look like they have bolts in them... Did you move or rotate the whole ship with bolts locked out? Won't be able to check my own setup til later, but has this happened to other designs? If it has, you may have found a bug.
The "needs more bolts" message on a beam is a leftover from when bolts and connection plates were used instead of welding. I think it basically means your beam hasn't welded properly, though there are other messages about that, too, so there's probably some particular circumstance that pops the legacy error message instead of the "beam needs to be welded to two others" current one.