The shop was lazy/ran out of the correct tube. If there was originally a schraeder tube in there that's what it should've been replaced with. In practice it won't affect anything except when you pump up your tires you might need 2 different systems (or a schraeder adapter for your presta tube if you use an air compressor.)

It's possible that the smaller presta valve will poke through enough to pinch itself on the inside of the rim. You'll also notice it losing air faster than the schraeder valved tube. I'd say get the correct tube and keep the presta for a spare to carry it with you in case you get a flat.

The difference in widths isn't major enough to cause any problems. Tubes are pretty stretchy.