After following the 3 step procedure for the tank sealer, which looked great, I was sanding and painting outside of the tank. Some water got into the tank during the process. I'm now seeing some small rust spots appearing inside the tank. Should I be worried, or do some sort of cleaning to see if this is an issue?

Please post some pictures. The entire inside of the tank should be 100% coated with Tank Sealer which will prevent so you might have rust staining over the coating. The other option is that the inside of the tank was so coarse that the Tank Sealer could not properly coat all of the peaks and valleys. Once we see the pictures, we will be able to tell and provide you some feedback on how to proceed.

Couple of shots inside tank. There's some dust and tape that got inside after coating, but the small rust colored areas appeared after some water got inside at least 4 days after coating.

Please take a wire coat hanger or something similar and unfold it and then poke those areas. When you poke, do you feel the tank or a coating?

 

You do have a very coarse surface on the inside of your tank so it may need another coat of Tank Sealer to cover all of those peaks and valleys but we will know more once you poke those areas.

 

We are looking forward to your reply.

I poked at the spots with a metal rod, seems solid but coated. I used a soft brush and a bit of simple green and the spots seem to be coming clean. So maybe just some surface spots from the exterior sanding water that got inside?

Yes, that is what it sounds like. If the surface is coated and solid, the rust spots are surely coming from somewhere else.