It's the underlayments/flashings/drainage planes that keep your house dry with stucco. With a traditional three coat system with the scratch/brown coats being portland cement follwed by a color stucco coat, it allows moisture to penetrate, but is stopped by the underlayments/flashings that send that moisture down and out by way of a weep screed flashing. It's important that in your case with the roof to wall connect, to still have a way for that moisture to have an avenue escape. It sounds like a flashing failure. Caulking and "waterproofing" will only be temporary fixes. Your best bet is to have the roofing pulled back along the roofline to wall connect and repair the flashing. The best method is to install a weep screed flashing up off of the roof on the wall and install step flashing when re-shingling tucked in behind the weep screed. Unfortunatelt this means pulling the stucco coats up enough to flash out properly, then patching. The weep screed allows the miosture to run down and out to the roof, but is stopped from penetrating the roof by way of the step flashing/roofing.

That's correct, the roof is probably leaking because the flashing wasn't stepped properly or the stucco does not have a proper weather barrier under it. Adding caulk or a stucco seal coat is a poor repair because it is not only temporary and could result in a greater expense later.