I've been having a same issue. The dealer had my car for a week.

The answer they've heard back was that all of the GDI engines (including, but not limited to Turbo) have problem with high amount of ethanol in gasoline. I've been told to run out the current tank, fill it up with 93 octane top tier gas (http://www.toptiergas.com/retailers.html), run through that high octane tank (just 1 full tank), and then I can go back to regular octane gas afterwards. I've been told to avoid lower quality gas (Wal-Mart, Sam's, Valeros, etc.).

I'm running Shell 93 right now, and not having any misfire issues I can feel right now. For some reason, I can go back down to 87 octane after this tank. We'll see what happens.

 

UPDATE: Hynudai replaced ALL fuel injectors on the fifth attempt to remedy this problem. It's been about a week and so far so good. Runs fine and no engine light.

 

Does anyone have an update that had all the injectors and fuel rail replaced to fix the re-occuring P0303 (#3 Cyl Misfire) code and check eng light? Did this work and for how long?

I've been through the guantlet to include just replacing #3 injector.

Thanks