How do I Unfilled these holes a copy and pasted from one side to the other and somehow it filled all my holes
If SketchUp automatically makes a face when you didn’t want one, click ONCE with the select tool on the face and delete it. If you click TWICE it will select the face AND the surrounding edges. That’s how you delete the hole itself.
I’m confused. Is the mesh a group or component?
If it is, then it is simply sitting on top of the surface behind it - no interaction.
If it is, you will have to explode the group then remove the surfaces created when the mesh and the surface it is on interact.
I’m confused as well when I move it over the mesh is empty like it should be as soon as I put it back on the face it blanks it out. I can’t delete inside the match. And It’s a group not a component
Until the group is integrated into the surface it is on (by exploding it) you won’t be able to remove the surfaces inside the hexagons.
How do I integrated into the surface?
It would really help if you’d share the model with us so we can see the exact setup. The heavy profile edges of the hexagons indicate that their geometry has not merged with the face behind them. There are a few different possibilities as to why that is. When you get them to intersect with the face they will display as thin, non-profile edges and you will be able to select and delete the faces inside them.
Explode the mesh (make sure it is sitting directly on the surface behind it) and new surfaces will be automatically generated
Thank you Dave - that was a much clearer response than I was able to generate. 
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Click in sequence on the scenes tabs of this SU file for ideas.
Part with arrays of holes.skp (3.4 MB)