Zach,
Whats "wrong" with it (imo) is that as the caulk loosens, moisture, food, and bacteria accumulate.
Each time the counter is wiped down, bacteria can be wiped from the joint back on to the food prep surface.
(Not to mention once the waterproof calk joint fails, moisture gets between the pieces, which then swell, grow mold, and rot...)
Moulded 1 piece counter/backsplashes are available, but they cost a couple dollars more, so most high volume builders don't use them.
Rob