Normally , I uses "where the bullet standing" as the hitbox reference (center) in top-down view , to make the bullet have its "thickness".
I think the weirdness is there's no shadow of player or bullet , so it will make you confuse and leads to "why the bullet didn't hit me" thoughts since you don't know how "thick" is the bullet.
Maybe I will update it after the game jam ended. Thanks for your feedback ^^.
EDIT : I found out what you mean of the weirdness of hitbox. In short , they were rotated and leads to unwanted behavior.