Welcome to Android Central! If we're talking about the same thing, the FBI scam is usually a popup that appears while only using the browser that holds the browser hostage, but only while you're trying to use the browser. I don't think the usual FBI scam causes the device to boot into Safe Mode.
If you're getting a popup that's holding the device hostage, tap the Home button, then go to Settings>Apps>All and select your browser. Now Clear Cache/Clear Data, and Force Stop. Open the browser again and see if the problem remains.