Instead of saying season two on the cover, it says season one. This is likely due to the reason that the first two episodes weren't an actual "season", just two pilot episodes, therefore making "Season Two", "Season One".
On the cover, Lloyd has on the green ninja gi, but instead of short legs and no shoulder pads like in the show, he has shoulder pads and normal legs. On the cover, all of the characters look like their design on the sets.
Also on the cover Jay is holding a weapon from his boster pack instead of his primary weapon in Season 1 The Nunchucks of Lightning.