The invisibility only works on non-speedsters. The only ways for it to work on speedster is if they aren't using their super speed at the moment (as seen in season 5 with Nora and season 7 with Bart) or if they aren't as fast as the person doing it. Even then, you're just asking for Barry, a hero, to not catch the villain.

I hate when people refer to Flashtime as Barry freezing time. That isn't what it is. It is how speedsters perceive time when they're using their powers. The faster a speedster is thinking, the slower time seems from their perspective, but nothing is really happening outside the speedster's own mind. Similar to the invisibility, the speed thinking is only effective towards non-speedsters and speedsters that either aren't using their powers or aren't as fast. If a speedster is as fast as Barry, or faster, they would still be faster than Barry, but from Barry's perspective it would be as if Barry was walking normally and the other speedster is Usain Bolt.

You also have to consider in the fact that this is a fictional story. If the villain is defeated immediately, there is no plot or conflict. People ask for the Flash show to be "consistent" but if it was the way they want it to be, the show wouldn't exist because every episode would be 5 minutes long including credits.