I think I know what you mean. Is it the case where you go to place one of those "crossed-circle" dimension control points, and you place the cursor over the location where an intersection, corner, hotspot, etc. should be, the check mark appears, and you click, only to find that the dimension control point is not actually placed on the corner, hotspot, etc but actually floating out in space near it? And it's only readily apparent if you zoom in for a closer look? I'll post a picture next time it happens to me.
I'm not exactly sure why it does this, but I've found that you can "tab" through the elements to make sure you have the proper one highlighted (and thus selected) before you click to place the dimension control point. That should help a little bit.
Also, you can snap to points on visible ghost stories when you're placing dimensions, so if, for instance, a wall is slightly offset from the wall above or below displayed as a ghost story, the dimension control point could snap to the ghost story wall. So later, when you don't have the ghost story displayed, it will looks as though the dimension is dimensioning an odd point in space.
Or, the "odd spots" your dimensions snap to are actually "static." In other words, when you were clicking around to place the dimension control points, it's possible that the odd ones were displayed as "crossed-out squares" (static) rather than "crossed-out circles" (associative). If they were squares, then that might also yield the same result--dimension lines measuring off into nothing-ness.
Of course, I'm using version 10, so who knows. Hope it all helps.
Keith