This has been an issue from Alpha. Madrid (and probably all amphibious vehicles)have a major flaw when amphibious. Right now, when they are in the water, they use propellers. When on ground they use wheels. The problem happens when the wheels get triggered to soon or too late.
They can only get out of water if there is a steep incline where their wheels touch land. If the land under the water is gradual, they get stuck. It happens because they wheels touch land but the propellers stay on. Since the wheels aren't moving, the Madrid won't move. Other times, the wheels get triggered when part of the vehicle is still floating in water and it gets stuck because propellers turn off. This happens mostly when vehicle hits ground sideways or when a rock or land sticks up. I say this happens "ALWAYS" because it always happens during those conditions. If the conditions are perfect, then there is no problem.
Waypoints add to this problem. Most of the vehicles that make it on land get help from their own forward momentum. Their forward speed helps carry them from water to land, increasing the chance of their wheels grabbing enough land. Waypoints in water cause them to stop and get stuck if waypoint is close to land. And that can't be avoided because sometimes that waypoint is needed to make the vehicle go where you want or else they find a long route around.

The problem can be fixed easily. Just let the wheels move when propellers are on. Having moving wheels while propellers are on help get over rocks.
ONE EASIER FIX= Give drivers ability to change between propellers and wheels. That would probably be more realistic, but AI will still have trouble.