Ive had a few, some my fault some engine bugs.
The 3.4 version of godot failed to export HTML correctly. The sound was choppy and the keyboard events were dropped after losing focus. Even after clicking back on the game. The solution for me was to use 3.3.4, which worked perfectly.
Some of nodes used a particle2D process material. Changing the speed of the particles in one instance of this node affected all the others. To be precise, the last process function that was executed affected all the others. The solution was to make the resource local to the scene. I have seen this button many times but didnt understand it up until I ran into this issue. Also the same for some collision shapes.
Other than these it was pretty straightforward.