You can hit the Plums as long as they're not flying above babies, and if we're talking after one loop, you definitely should have some way of countering, whether it's active items or familiars.
"'ve just never encountered this problem" is not mean this problem is not existent, and i am not sure what you mean " block the enemies that block your shots", you mean kill that? Or use some baby like "Cube of Meat"? Whatever which is you choose, they all lead to you place more baby in a line and plums will easy to fly