Villains should always, always have a Plan B. And if possible, a Plan C, if their powers desert them.
Jamming and Jacking
Here's a scenario probably none of you are preparing for: you're doing a heist, you're about to get away, and suddenly.. the power leaves you. It feels like shock, the oxygen draining out of your tissues. Suddenly you can't run fast, or fly, or whatever you were planning to do. And none of your other powers work. And there's someone watching you, and smiling really scarily.
What has just happened to you is how about 10% of all villain captures a year take place. Power nullification, or "jamming", is a really obnoxious thing to have happen. But it can and does happen. How do you get out of it? Preferably by having escape routes that don't depend on your powers being active at the time. Oh sure, you can use them beforehand to arrange it, but a hidden getaway car can't be jammed.
How do you deal with it? It depends entirely on the abilities of the jammer. Sometimes you just need to get out of range. Other times your body's metabolism will get rid of it naturally, and you just need time.
The worst thing to deal with is the subset of jammers who acquire your power at the same time - called jackers. If you've been jacked, all you have is your natural healing factor to protect you. If you are lucky, you'll have more familiarity with your powers than the jacker. A few paranoid villains, or ones with a dedicated jacker hunting them, carry their own countermeasures around with them. I can't stress enough how unwise this is unless you actually think you'll need them - but if you do, it's the smart thing to do.
Remember how I said earlier that athletic skills like parkour and martial arts are important for any villain? This is one of the reasons.
Loss of Confidence
Powers come from your body and mind. Like anything else, from doing math to having sex, performance anxiety can rob you of your abilities temporarily. New villains who rush to do their first caper without practice and planning sometimes get so scared that they lose power. Well, at that point the cops just come in and bust them, obviously.
There's nothing to do about this but practice, train, and psych yourself up beforehand. Get in the spirit of being a villain, get that mindset firmly in place, then go do your caper. You'll feel incredible. Psychologists call this experience "flow".
If you lack this, there's probably not a lot you can do on the scene. Afterwards, of course, you should be incredibly motivated to get practice. But "afterwards" in this scenario is usually "in jail", so don't go in without feeling ready!
Mr. Big's words of wisdom: proper preparation prevents power problems.