: I put a coat of epoxy on oak plywood, first time to use it on oak.
: There was one layer of dry sanded but clean light oak stain on
: the wood. . .

Might this be an oil-based stain? After you sanded it did you wipe the area with a damp cloth? a cloth which is wetted with water? a cloth which was wetted with paont thinner or some similar solvent? If so, then what you have might be a slight oil contamination of your epoxy. The stain soaks in deeply into the light grain areas, and it is absorbed way down into the pores of the wood. On the darker grain areas, though, the wood is harder and less porous. It could be that even after your light sanding some of the colorant in the stain remained on the surface. it doesn't take much.

If this was just a test, try another test on a fresh piece of plywood. Use your stain, sand and use a mix of ammonia in water to remove any residual oils on the surface. This may raise the grain, so you may want to do a little resanding after it dries.

: wood had been at 70 degrees over night but brought
: into 60 degree shop a hour before epoxy coating.

This doesn't sound like temperature was an issue.

I think the pits got there by floating up to the surface of the epoxy and forming tiny oil droplets. The surface tension pushed the resin aside, leaving a droplet of oil just under the surface of the epoxy. When you sanded you removed the top layer of resin, exposing the oil droplet. The oil was dispersed with the sanding dust, but the hole it was in remained behind. That is a pit. Lots of tiny oil droplets give you lots of pits.

: After sanding, the light grain was fine but the dark grain areas
: look pitted. I can't feel any difference with my fingertips, all
: feels smooth after 200 grit and orbital sander. Definitely
: "looks" like numerous small pits.
: Anyone else experience this or have an idea what caused it. Not
: sure of an alternative other than to sand down to the wood and
: start over.

Why sand that deep? For that matter, why sand with such a fine grit sandpaper? 100 grit would be fine. This is only a first coat and a little texture to the surface will give the next coat a good bonding surface.

You are going to put on a second coat of epoxy. It is always two coats (at least) to seal the wood. Right now your first coat has soaked deeply into the wood and is tightly locked into the pore structure of the cells. To get to "fresh" wood you would need to sand really deep--maybe take off 1/16th to an 1/8th inch. That is a lot of sanding, and it would also remove your stain. Epoxy can REALLY soak in !

Since your first coat has sealed the wood, and since you have already done some sanding, you are in great shape to put on a second coat. It won't take much resin. You'll use far less than the first coat because it won;t be soaking into the wood fibers (those are already sealed shut by the first coat) and you want to put it on very thin so it doesn't run and put you into a position of needing to sand off the messy areas.

Go over the existing surface with a solvent to remove any possible oily contamination which is sitting at the bottom of those pits. Then wash it with a mix of warm water and A FEW DROPS of liquid detergent. use something like 4 drops to a liter. Very small amount of detergent. Follow this with a wash with warm water. The three-step rinse will not soak into the wood as it is pretty well sealed by that first coat of resin, so there is no worry about raising the grain again. YOur second coat of epoxy will flow into the tiny pits and should level itself off. It will also give you a thicker surface to sand back to get a super smooth surface. If you were to put on varnish at this time it would probably work the same way in filling those tiny pits--but if you want a waterproof surface you need two coats of epoxy, whether you varnish or not.

Hope this helps. Without seeing the surface I'm kinda guessing on a diagnosis, but it is my best guess.

PGJ