So, for example, you enter the wrong quantity (too little) when backstocking or when pulling. You enter 6, but there's really 7. Autofills pull 6, one's left but the system doesn't know it. Later on, the lone item is scanned when pulling another batch, the system didn't know it was there, so it adds it. This results in a baffle error.
Another way baffles are created is through M-delete. You scan some items in a waco but not all and then use m-delete. The items you didn't scan are now unlocated -- the system doesn't know they are there.
One easy way to see if something is baffled is scanning it in STO, the location will be listed but without a quantity. I believe baffles will also prompt you when pulling the item (Did you pull all from the location?)