(LWJGL) matrix stack object movement

so in my scroller game the player throws an object towards the mouse based off regular screen coordinates. This works fine, but it moves with the screen, not by itself. For example if i were to move the player upwards, the object would move in the same direction but move up with the player. Everything in my game has it’s own matrix because I need to rotate it with the mouse. for a top down type of game, how do i handle this annoying matrix stack?

This is a perfect example: https://www.youtube.com/watch?v=f504_TavOnU

when the player shoots the projectile moving the player shouldn’t affect it’s course.