Burrows are only used by one part of the game, they are 100% optional in that part, you can work around the problem, and it can't do any damage unless you choose to let it do so. Why wouldn't it be called minor? At worst it's a nuisance, and it's one which many (perhaps most) players will never contend with.
I suppose you could play and ignore burrows totally unless you have a civilian alert and need to consolidate your civies. Initially i started using burrows to prevent my jeweler from getting having rough gems lifted as this was interrupting his work entirely. This worked great but unbeknownst to me in the background hauling tasks where accumulating that where necessary but would eventually be ignored.
I found the burrows tremendously useful for streamlining automation or for keeping my dwarves out of caves which i now have to use locked doors for.
I see tremendous potential for them and it' kinda hard to go to a minimal burrow uses(for emergencies) when you experience their shortlived benefits.
I was never able to find the offending stockpile anyway , i tried covering the surface with a burrow as well as all the transitional Y layers incase somebody wanted to pick up a rock on a step or a dead rat that got killed on a stairwell.