How do I keep the opponent down longer so I can pull of a flying attack like the 5 star frogsplash or Flying headbutt which take I while to pull off. I could pull them off easy in every other Smackdown game except this one, is this some kind of glitch?
It's not a glitch, but it is a huge gameplay flaw. You'll have to get the opponent red in the head + body and hard whip them into the exposed turnbuckle. That should give you enough time to pull off a high flying move.
If it's a no DQ match or the ref's down, a chair finisher should keep them down long enough. Busting them open almost always works as they start selling like there's no tomorrow, giving you enough time to hit a top rope move.