I have a Pi 4 8 gig using emulation station and it’s in an arcade 1up.
Does this mean you're using RetroPie ? Please give more details about your system, as explained in https://retropie.org.uk/forum/topic/3/read-this-first.
When navigating the menus all controllers work fine. Once I enter a game to play, only the Logitech controllers work.
If the game is a max 2player game, then only the first 2 controllers will work. What game/emulator are you using ?