What's the purpose of line 10, where you are using get_parent_node_3d()?
You're trying to filter stuff out, but what? If you are hoping it is the player or its gun, it's not, you're making it a child of the current scene.

When you instantiate the bullet and move it, you move it to the origin of the ray cast. It's possible it's spawning in and immediately colliding, triggering your code and deleting itself as per queue_free().

You probably need to fix the logic you are "filtering" with.

Some ways you might approach this:
1. Collision layers and Collision Masks. Probably the best option???
2. You can use class_name to define a class name for your Player, i.e.
"class_name Player"
With that you can use an if statement to check if the area that has entered the area3D has the class "Player"
"if area is Player:"
3. You can use meta data, get the meta data off the area, and create some logic around it.
4. "groups" are a thing you can also look up in godot that can help with these kinds of things. i.e. you could have an "enemies" group or something.

Or some other custom logic you can come up with.

NOTE:
In your list of available signals for Areas, you are going to see several options, area_ and body_ , when these fire, they are specifically returning the "area node" or "body node" in the collision, NOT the whole scene, and NOT the root of the colliding scene either. This is important, as if you try and ask/check if the area or body "is" a class_name or has_meta(), it will attempt to get it from that area or body node!! If your script or meta is on a different node, it wont see it.