The underside of my Mayayan pyramid’s top has these faces which appear to be Z-fighting but are also exposed outside:
(The same selection appears like this outwards)
Is there any way to fix these extra extrusion faces?
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You can select faces and delete them (or edges, or vertices).
You can also try to dissolve vertex doubles.
But your problem occurs at extruding edges, thinking they are faces.
It happens when you try a lot, without having a plan of which face needs to be extruded to get the wanted effects. You can also decide to just add a new object. Not everything needs to be in the same mesh data.
You can start over or manually clean up your model. Which is a ‘normal’ Blender task for modeling. From concept to final model.
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I didn’t extrude the edges, I extruded the faces earlier. Seems like I extruded where I should’ve simply moved?
I’m dissolving each edge carefully. So far, it works.
EDIT: Marked as solution since it solved this specific problem. Many more seem to be bunching out, but that’s just life. 
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A general merge by distance can cure such issues, along with a subsequent face direction check.
Ah, I’d tried that before, but ended up doing it once I’d dissolved all the edges to merge the vertices that remained stuck out.
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