Recently my trackpads tracking bugged out and it decided to use my master ball on a Munchlax. Having it so close to the top makes it easy for me and many others to miss click it. With the level and net ball being lower in the item hierarchy, I think it would be better to move it away from one of the most common click areas. Or have a new UI pop up to ask the player if theyre sure they want to use their master balls.

I can also think of a phone where the touch screen is kind of bad and some areas of the screen doesn't work properly, that could also be a case where the masterball is used instead of a regular pokeball. Just to give more reasons to your suggestion!

yesterday i threw a masterball on a normal nidoran m for mistake :D

 

and that happened on phone :D