General question re: the settings; there are hundreds of menu options... is one of them a way to stop a dino from being active while the ball is trapped up (e.g. most noticeable during raptor lock or control room). You can easily lose what feels like an eternity (even if it is ~5-10 seconds) when the ball is trapped up.
Not a huge deal, but can be a big problem with fast dino's. e.g. I feel T rex can eat two people in the time it takes to get the control room animations started, picked a mode etc.
The obvious fix is "don't put the ball there when you don't want it to be there". I am just used to so many games pausing timers when in single ball play, and the ball is obviously stopped due to a game function. I was surprised to see the dinosaur's still marauding around while the game was otherwise stopped.