We had this exact problem. The GC, who is also a plumber, didn't pay attention to my sink specs when he installed the drain pipes. My sink is 10" deep, plus the 1.5" counter, so the drain is much, much lower than in my old 7" deep overmount sink. When the disposal was first installed, we had almost an inch of water standing in the bottom of it unless we ran it for about 30 seconds after the water was turned off.

Obviously, this was unacceptable. We complained and he came back and fixed it in less than an hour. He just needed to lower the point where the drain pipe for the disposal met the main waste pipe in the wall. It has worked fine ever since. He offered to pay our cabinet guy to make a panel to patch the place where he had to cut further down in the back of the base cab. I haven't taken him up on that yet, but I may.

Hey there,
Measure from the center of the pipe stub coming from the wall to the top of the countertop (or planned height). Then, there should be spec. sheets for both your sink and disposal available from the manufacture. Take the overal height of the sink + thickness of counter top + dimension from top of disposal unit to center of exit pipe(*). The sum of all of these should be less than what you measured. This ensures water will flow, ie. water flows downhill.

(*) sometimes manufacures will specify a large dimenion to ensure water does not sit in disposal, spec. sheets will note this.

Drop me a note if I'm not making sense. I'll make you a sketch of your setup if you like. It's time I gave something back to this forum!
BR,
RO

"Rus_ut" has it exactly right. Not hard to figure if you can get the specs on your sink and garbage disposal. Also make a note of the D/W drain as well. Depending on how deep your sink is, and how high your drain is, you may be able to find a "compact" style disposal that will work without modifying the plumbing.