charge needs you to charge it up by holding down the attack button. Yeah probably needs an explanation about it somewhere especially for people who usually like to rapid tap
Every time you pick up a weapon all future weapons you get are leveled up to encourage swapping between them a bit more instead of camping one. The non weapons upgrades that are permanent stack but dont get better (you just get more of it aka two orbital powerups = 2 orbitals)
Which x button did you click and in what phase of the game (main menu, in game, etc.). The one in the stat window? Or did you exit a different way