If it's a perfect clone of an existing Pokemon made using certain means, it's usually virtually impossible to tell which is the clone and which is the original. However, there are sometimes certain indicators which show that a Pokemon is hacked (and hacked into the game badly), such as impossible movesets and the like. In some occasions you can't trade a hacked Pokemon via wifi (I had a friend hack some breeding dittos into his game and tried to WT them out, but he messed up and so he has a box of untradable Dittos now).