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I recently adopted two RES from the local Humane Society. They live an a well-filtered, outdoor pond, with access to natural sunlight and dry basking areas.
They've also been actively swimming/walking/eating/defecating on a regular basis.
Essentially, they seem perfectly healthy, until I took them out of the pond yesterday.

This was on the male's shell:


This was on the female's shell (the pinkish patch to the right; it's darker in real life):


I've gone to a reptile veterinarian, and she said that there isn't very much need to worry, as long as there are no significant behavioral changes--since these wounds are very small, in comparison to the turtles' overall sizes.

Any advice is much appreciated!

Do you know if these are new injuries or from when they were still at the humane society? Are the areas sensitive to touch?

The male's injuries were present since the Humane Society, but the slight redness is new; the female's appeared two days ago.
None of them are sensitive to touch--I've even (gently) run some clean water over them, and the turtles didn't even seem to notice.

Did the vet say what the problem might be?

The female's shell issue had not appeared at the time, so the doctor's advice was mainly directed toward the male's care. Since the turtles came with very little background information, she couldn't make any definitive diagnoses--she only said to watch out for behavioral changes (i.e., lethargy).
However, turtles are very adept at "hiding" illness, so I'm not sure if that's even a very reliable parameter.

are you going to an exotic vet or a regular vet?

Overall, the clinic has a few vets, each with their own specialty (i.e., Vet A usually sees dogs/cats, Vet B usually sees birds, and Vet C usually works with reptiles). I went to see "Vet C".

my rescues had some serious scars when i got them 2 years ago, now they are barley visible, a healthy diet and proper basking will help with the shell issues.

Sounds good! Thank you for the advice. I'm thinking of adding frozen vegetables to their diet, as well--is that generally well-received? (i.e., corn, peas, carrots).

I'd stick to fresh veggies.

I'll start integrating some fresh vegetables, then.

Another update--the male's "holes'' look smaller! The areas that were previously "open" also seem to have been "filled in" with hard (but whitish) shell. Should I be concerned by the coloration, or is it just trying to heal over in layers?

Keep a close eye on it. Have you felt it? Is it smooth?

I've felt it, and it is quite smooth--it feels the same as the rest of the shell (which is healthy). The only difference is the whitish color.
The slight redness around the area is nearly all gone, as well.

Your basking dock is rough, hard, or solid?

They have two different basking areas--the first is a layer of slate (textured, but by no means rough). The other basking area is just a large-sized floating platform that are typically sold for aquariums (the rods and suction cups have been removed).