It's not really a problem as they disappear soon enough for me, or I pick them out, whichever happens to happen first.
I wouldn't really worry about fruit flies, anything bacteria or pathogen wise would more than likely be annihilated within a few seconds of contact. The salt levels on the outside would drain all the moisture out of the cells (the cell would be in a hypertonic solution and the water would move out to balance (killing the cell)).