If you are ever doing anything like `load("res://EnemyScene.tscn")` where you are loading a sound effect, scene, or script at runtime -- that might cause it. I'd try to cut down on runtime loading of stuff, and `preload` where possible, or spawn nodes when your game starts and then switch them visible/invisible.
Unfortunately I'm not 100% sure what causes these issues -- for me, it just seems to occur during scene transitions or when a lot of things are loaded. I'm sorry.