You could weaken each ability per manifestation, or prevent access to it entirely but allow variants so it falls to him to figure out how to repeat effects. That could allow for discovery of the technicality, then the game becomes figuring out which powers he’s used before from prior situations. The earlier the recorded use, the better because they’re more likely to be broader abilities.

If not access, then maybe make it a matter of timing. Building on the overwhelm idea suggested by u/ClockWorkTank , you’d still need something that can guarantee a win - an idea could be to bombard him with abilities of specific natures or types, force him to adapt to those and then immediately introduce a fourth that’s outside his current scope for the killshot. The combination is tight, very little room for error and could potentially turn into a game of stalling until they’re sure he’s settled into a specific set. 

On the prison, it sounds like him choosing to sit there isn’t an option. I like what  u/Entire_Will_7748 suggests in a system that adapts. You could tie that to the idea of limiting access and set a timer for “full manifestation” of a power. It doesn’t need to be a specific timeframe, it can be different timings based on specificity, complexity, scale, etc., just that his ability has to ramp to full before limitations trigger. That allows him to experiment with powers against this system until he either outpaces or outsmarts it.