Of course Beyonce has songs that have flopped, every artist does. Even incredibly talented and legendary artists like Queen have songs that flopped. When you look at the number of songs Beyonce has released, it is not surprising that a lot of her songs did not do as well as she and her producers thought they would.
This happens for many reasons which may or may not even include the talent of the singer. It may have just been a different sound that did not translate well to fans or it could have been that another artist was also releasing music which just eclipsed it. Some examples of flop songs are 7/11, Video Phone, and Kitty Cat.