No it does that to me too. When I walk in the double grass and two pokemon appear you have to defeat one to catch the other. Also you cant attack with one pokemon and try and throw a poke ball at the same time.
I think it's because I ask pokemon A to send an attack then pokemon B (or me) to send a ball as the person above said.
Which is annoying
When a pokemon is near critical and awake you know that if you threw a ball it would still miss so you need Pokemon to put it to sleep or something to raise the chances of it being caught but you get poke-blocked by some smart arsed game mechanic ¬_¬
Waiting patiently for UnKarted to be announced since 4-Dec-2009 http://us.playstation.com/publictrophy/index.htm?onlinename=Ajescent