I've seen "spooky" behavior before by doing:
Filter - select objects in query
M, S to move stuff around
SHIFT+C to deselect
Wait, why are some parts all kinds of wrong?
CTRL+Z+Z+Z...
What happens is, if your query included locked primitives owned by a part, it'll still move them, even though they're locked (usually with a This Selection Contains Locked Primitives... popup). You could move all primitives inside a part, giving the same effect as a severely off-center origin. Or, if even just one primitive is left in its original position by not having been selected, the extent of the footprint might end up really huge, which might be what happened here?
Updating the affected footprint(s) or deleting and replacing them is probably the best, yeah.
Tim