Viggle shared some great info on their blog recently on ensuring that you are checked into the correct episode
"Viggle’s technology has a very high hit rate in terms of recognizing the shows you’re checking into. That said, there are a lot of variables outside of our control…
We’ve heard some Viggle members mention that Viggle sometimes checks them into the wrong episode of the show they’re watching. This comes up because sometimes one episode of a show will have bonus points and others will not. To avoid this problem, we recommend checking in while the actual show is playing and not during commercials. Commercials vary from city to city which makes it very difficult for Viggle to accurately confirm your check in."
Hope that this info helps and for more information on Viggle Check this out here !