I depositted a bunch of bad pokemon I got from the catching contest and withdrawed the good ones, however when I tried to put either of them into the contest run it gave me an error that it couldn't select it and should report it to the staff team.

One of these had a regular ID, and the other had an ID of 0.

wait for 1 to few minutes to let the poke id generated first

There was indeed a bug regarding the pokemon select dialog, the team is currently looking into it.

 

 

In regards to the 0 id pokemon,

After receiving or catching a wild poke the client will display ' 0 ' as it's id temporarily, while the server saves its data and generates its unique ID from millions of pokemon stored in our database.

It results in a delay as active session in client fetches data from our database intermittently. Give it a minute or few as suggested by our fellow player, @hahahaka.

A re-login will refresh the session and the client will instantly fetches a fresh new data. Thus, includes the generated ID of your newly caught pokemon.