On this aspect, many supers systems have mechanisms to model “lack of control”:
Naked “Activation Rolls”- unique to each power- are one common one. You gain control by improving your odds of success with that roll. Sometimes, activation rolls might be skills based, and certain skills may cover a variety of powers. A character who can alter matter at an atomic level might have to make an “Alchemy”/“Science”/whatever roll to get the result they want.
Side Effects that trigger when a power is used. This could be ANY and EVERY time the power is used, or only when there’s some kind of mishap with the power (like a failed activation roll). Increased control of a power with side effects could be reflected in reduced severity or frequency of the side effect, or both.
Attack powers might have to be targeted just like mundane attacks. A relatively uncontrollable power might be extremely difficult to use with any accuracy.
A character might not be able to manifest the ability at a consistent & reliable power level. Imagine having uncontrolled super strength that might usually manifest as merely doubling but occasionally being an exponential increase…or vice versa.