Where are you growing these tomatoes? It looks like you're growing them hydroponically? Do you have a better picture of the yellow spots? Yellow spots often mean nutritional deficiency, but I don't personally have any experience assessing and titrating nutrients for hydroponic plants.

I'm having a hard time seeing the fine detail in the images. If I had to guess, I'd say it could be sun damage. Did you recently put them outside in full sun without hardening off or get their leaves wet when they weren't used to full, unprotected sun?

Or it's possibly a pest, especially if the white transparent spots are like paper. Check carefully for small pests, like very young caterpillars, under the leaves, especially at night.

Maybe you could upload full-resolution pics to a service like imgur or flickr and give us a link? Unfortunately, gardenweb keeps images rather small.

Yeah I am growing them aquaponically. I assumed the yellow spots were some type of nutrient deficiency as it is very common, but what confuses me is the transparent holes, and since they are inside I doubt it is a best or sun scald.

Pests can get inside greenhouses easily. In fact, many pests are a bigger problem indoors because there are fewer predators to deal with them. Another possibility is some kind of chemical burn, if you are spraying the leaves with anything.

I did not know that, and I haven't sprayed anything on it. Do you think it could be late blight?

That does not look like late blight. Late blight lesions are typically dark, water-soaked or greasy looking and later turn dark brown. In humid environments, they'll be fuzzy with spores.

Here a link to a better pic http://imgur.com/Go4Zi6f

As mentioned in your other post of this question there are basically only 2 common issues with hydro grown plants - nutrients and pests. As GB and both posted your plants clearly have nutrient issues but only the folks on the Hydro forum here can help with that. It is a totally different and unique method of growing.

Otherwise one of the common GH pests, aphids, spider mites, other mites, fungus gnats, etc. - is the most likely cause.

Dave