Magic is modifying many plugins with its default configurations.. first i had to spend hours preventing my sticks turning into broom sticks and now this issue of magic instantly closing a GUI when i clicked some stained glass panes, in another one of my plugins. It does not happen without Magic installed. can someone please help me figure out what I need to turn off inside of magic to fix this?

server version 1.12.2 paper, latest magic

It sounds you have some incompatible plugins, this can be very hard to track down. Since you know magic is one of them, you probably need to just remove it. Sorry!