Limitations of hydrofoils
Hydrofoils are beneficial in many areas, but their usage is not applicable everywhere. One place you would not want to even attempt using hydrofoils, unless you are an extremely experienced operator, is on a river. Hydrofoils need a certain amount of water to be able to support the boat. If the water is not deep enough the foils will hit bottom and most likely cause damage to themselves, the boat, and possibly the passengers.
Another limitation that comes to mind is similar to a limitation of airfoils, namely they will stall when placed at too great an angle of attack. This could be a problem, but fortunately hydrofoils do not have to be angled to such an extreme degree in order to produce the desired lift. Since the density of the water is greater than that of air, the necessary angle of attack for a hydrofoil is minimal compared to what an airfoil would need. The definition of angle of attack is shown in the diagram below.
Other diagrams at http://web.mit.edu/2.972/www/reports/hydrofoil/hydrofoil.html
Another limitation of hydrofoils is the foil coming out of the water. If a wave is large enough to hit and lift on the original hull of the boat the hydrofoils will be pulled down away from the boat with extreme force. This could cause the foils to be ripped from the boat or cause other forms of damage. Also if the boat is moving fast enough to make the foils come out of the water (e.g. on the back side of a wave) the stability of the foils is lost and the boat may tip over or even be sucked back down to the water surface when the foils re-enter the water. This would happen if the front foil became airborn causing the bow to drop. The bow dropping would cause the new angle of attack to be negative, thus pulling the boat down rather than pushing it up. Another problem is ventilation. This is where air gets under the foil. Since air is almost 1000 times less dense than air, the boat will fall until it is supported by the water again. These are possible problems, but they can be almost completely avoided with good engineering design.