This is definitely a glitch.
Is this the first time it has happened? Like is it the first of something like your first Lillipup, first Pokemon encounter, first encounter on Route 3? Or has this just happened out of the blue?
It could be the shop you brought it from - Patrat and Lillipup seem like very early Pokemon, so I assume you have gotten the game recently. Have you bought Pokemon games (or just normal games) from the shop you got it from before? Have all the games been to your knowledge non-counterfeit? If the shop you get it from strictly forbid refunds, than you probably got a fake one from a counterfeit game seller. I wouldn't go back to it. If they are willing to let you trade in for another one, do so.
It might just be a glitch in the game. And quite an understandable one too, since it is a 'pkmn'. So it seems pretty reasonable and forgiving. If it doesn't happen again, I wouldn't bother worrying about it however if it happens more frequently then, like so, return the game.
Hope I helped. :)