Please see example picture: Image link for example

I've deleted the node segments between all 4 bottom nodes. And they somehow connected and filled the space between them. As you can see the highlighted part with red outline in the link above.

Is there a way to remove that fill?

There is nothing you can do about that - except you go Path->Break Apart to receive to separate objects which can have now different styles.

I've made the outline and the fill a separate object at the end. And rejoined the nodes for the filled one.

Not sure what your goal is. If you like to have both shapes in one object and both filled with color you need to reverse 1 path - then both paths have the same direction - that´s all.

I'm planning on making a bearded guy. It's complete already. I was just wondering if there was a method where I could delete the fill that was overflowing where the node segments were deleted.

I wanted to connect the side burns with another object bellow. So that the outline is not visible where the node segments were deleted. See pic bellow.

Image link

In my first pic the fill was overflowing and it would have gone over the eyes and nose of the bearded fella.