Very poor design to have built it that way, from what I can see in that picture it makes no since to have built out the foundtaion like that. It's a sure way to have leaks all around it. The siding should have been finished then the stairs go in. Looks like the stucco was run around the stairs that was already there.
Look at the right hand side of the door at the threshold. It looks rotted.
Reason being it's a cheaply made door for one thing, there's no sill pan under it to stop water from getting in on the outside edges. I'd also bet there's not even any form of flashing under it.
If it was mine I would remove that door and install a fiberglass door, vinyl jambs, adjustable threshold, flash the bottom of the opening and install a jamb sill pan, then reinstall the door. It would never leak again.
You only think this is not doing any harm. It's going to rot out the floor joist, rim joist, foundation plate, and cause black mold or fungus to form if this allowed to go on.