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So here's my render:

render

and here's my compositor node tree:

nodes

The green spheres are on a separate layer from the rest of the ship, so I can apply glow and blur effects to them, without affecting the rest of the ship. Why aren't the green spheres covering the holes in the ship mesh?

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The mix node uses the alpha channel of the top input exclusively. So whatever is transparent in the top input will be transparent in the output.

The solution is to use an alpha over node as you mentioned, or mixing the alpha channels with a separate mix node and then plugging that into the factor.

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I think I fixed the issue by substituting the last Mix node with an Alpha Over node. That appears to have gotten rid of the holes, but I don't know why. If anybody's got either an explanation, or another fix, I'd love to hear it.

Thanks!

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