With how flying is now if you get into a battle with a pokemon midair your pokemon keeps flying with you in the direction you were following a flying pokemon in. When you try to catch something like a legendary with a masterball off the bat, your player is far away from the chunk you threw the masterball in which causes you to be stuck waiting in battle and the pokemon you are catching actually despawns. You used to drop off your pokemon when entering battle and everything would be fine. Now you lose the masterball and the legendary if thats what you are trying to go after.

Confirmed! Forwarding to Internal! Thank you for your report!