If you are really bothered with AI spies you can use Cryptography policy and use a spy with Polygraph promotion on counterespionage... -3 level is huge
The problem is not catching the spies, its that my spy stops counterspying after catching/killing an enemy spy. The AI has 2-3 spies stacked up and they all pop on the same turn so I catch the first one and my spy calls job done for the turn and the other two succeed.