We do periodically see problems like this, and a minimal case to reproduce the issue is always helpful, since the occurrence tends to be specific to a very particular combination of items and their resultant horizontal spacing. The nature of the problem is typically that the profile that Dorico maintains of items above and below the staff for the purposes of avoiding collisions with the adjacent staff or system is either being updated or cleared incorrectly, with the result that a tiny bit of the profile ends up in the wrong place, and then when an edit happens, an item is “tucked” against that profile and ends up moving outside the spurious bit of profile that has been left behind. If it is the item itself that is responsible for the spurious profile being there in the first place, then that problem is often compounded by subsequent edits, as each edit leaves another bit of profile there, and the item then gets tucked against that, moving it further away from the staff each time.
You don’t need to delete the item to cure the problem: you just need to close and reopen the layout. But if the conditions are right for the problem to be triggered, the bug will recur when you make edits on that system.
As I say, having a reproducible case is necessary for us to fix this kind of problem, as it is always specific to a particular combination of items and their actual positions.