I beleive that this is expected behaviour, as Sublime seems to track the dirty state of the file based on the list of edits that have been applied and not on their cumulative visual effect on the file contents.
So for example pressing ABackspace makes the file visually appear the same (and thus apparently not dirty) but there are still two unsaved edits, so it's still considered dirty.
On the other hand, pressing ACtrl+Z (i.e.
Undo) removes the original edit, which takes the file back to an unmodified state and correctly marks the file as no longer dirty.
Aside of that, Sublime also always saves the file when you press save, even if the buffer is currently considered unmodified.