When Kara first sees Kal on Earth, she furiously demands medical attention. No, not for me, for him! Look, something is wrong with him! He’s clearly not well, don’t just stand there! He’s not supposed to look like this! What’s on his face?!
That’s how Clark figures out that freckles are not normal for Kryptonians.
He didn’t have these as a baby, Kara shrieks. He was perfectly healthy, not diseased! What have you done to him—what did they do to you, Kal? Are you sick? Are you…no. No, please. Is this my fault? Because I wasn’t here to protect you? All of Krypton is gone and the only other person left is my baby cousin and he’s dying. What have I done?
It takes a while to calm her down and show that Clark is more than okay. Kara, your baby cousin is perfectly healthy. The freckles are…
Huh. Well, now that everyone thinks about it, they don’t know what to say about Clark’s freckles. He’s had them as long as they’ve known him and no one’s ever given them a second thought. Clark doesn’t remember not having them. One of his earliest memories is of Ma tracing the patch on his left cheek, whispering about the way the brown flecks were like constellations on her perfect little star child. He’s never considered that he might not have had them before coming to Earth.
Kara assures him that he didn’t have them. She remembers him as a baby like it was just yesterday—because it was for her. Kal was the happiest baby, all gummy smiles and sweet giggles. He was a chubby little thing with wild curls and wide, curious eyes. More importantly, his squeezable cheeks? Not a mark on them. Whenever and however these things happened, they weren’t there before he got to Earth.
In the hours it takes for Clark to fly to Smallville and collect his childhood photos—all the them showing him with freckles—and for Bruce to complete an analysis of his skin cells, Kara’s panic increases tenfold. She catches sight of her own reflection in a window and sees something on her nose.
Freckles.
It doesn’t take long to figure out that this is just how Kryptonian skin reacts to yellow sunlight. Krypton’s red sun didn’t stimulate specific cells in the uppermost layer of Clark and Kara’s skin. But under a yellow sun? The cells flourish. Under a microscope, it looks like the cells are actually storing energy in little pockets of melanin (or whatever the Kryptonian equivalent of melanin is). To the naked eye, on Clark’s cheeks and Kara’s nose? Beautiful, perfectly benign (if not beneficial) freckles.