I can't explain it well but please try to understand the situation. When i try to change my team especially the starter pokemon i'm going to use, the pokemon that i'm about to switch will be doubled and the pokemon one the first slot before i change my team will be gone. Example, i want to change my starter which is currently gengar to my pokemon on the fourth slot which was flygon. When i do the switch, flygon will be on the first slot and still got a flygon on the fourth spot but my gengar will be out no where. Is it bug or what? Pls answer?

Yes you are right it is a bug that doubles the pokemon in your box and you can but it in your team both pokemon so yeah its just a bug its nothing really major to be worried about

Go to your pokemon and click the remove pokemon 2-6 then log out of the game and log back in again and then put the pokemon you want back on to your roster,this usually solves the problem.