When I was trying to catch Zapdos (I asked a question about before), I decided to use a Wobbafet (sorry horrible spelling!). I put it in my 1st slot for my party when I ran into Zapdos, it still ran away. Is this normal? Please help me! Thanks! :)
Yes, it's normal.
The three legendary birds will run away, no matter what trapping devices you try to use on them. They will run away for about 20 times, and you can track them via your Pokedex. When they finally stop running, they'll be at the Sea Spirit's Den for you to battle.
Serebii - X&Y Legendaries