Each fly should have a Raycast to check tilemap collison, so you can prevent them from going further. Regarding spawning below floor, you could place the spawner game objects placed in the sky and activate/deactivate them when they enter/leave the camera. At least I'd do something like that in Unity, but Godot should have something like that too
I haven't done a lot with raycasting. I'll look into that. I do handle collisions with the tilemap via the CharacterBody2D obviously, is it the same with the raycast? Like it would give me a collision that I would then be able to work with and get tile positions from, etc...? As for the spawners, they are in the air, and they have a radius for spawning. I should likely have used that same raycasting to identify if an aniticipated spawn location was a valid location before spawning the fly. Other than that, the spawners only spawn fliws if the player is within a certain radius, which, in hindsight, I probably should have just made if they were in-camera. I appreciate the feedback and advise!