I feel you! Two days before the end of the game jam, I added a pause menu, but it had a bug where, when I unpaused, the physics engine would go crazy and lag the entire game, making it unplayable. I wasted 4 hours just to find out that the part that detects collisions in the Godot engine really doesn't like when you set the engine time scale to 0. and detect around 10,000 new collisions every time I paused. While I had to set it to a very low number, like 0.001 Instead. I was considering removing the pause menu completely, as I was running out of time and it rendered the game unplayable.