My dog is pregnant but she got pregnant recently as of 2 weeks ago. At night she whines. What could be the reason ? Are the puppies kicking or making her feel uncomfortable ?

At 2 weeks in you wouldn't even know for sure if she is pregnant.

Time for a vet check, the male may have done damage to her or she could have a medical problem making her unwell.

She's pregnant for sure, last time I was home her nipples weren't engorged and when I came home they are hanging & engorged and her stomach is getting bigger. She could possibly be further along.

Still not a clear indication. Females can have what is called "phantom pregnancies" which is where they mimic the symptoms of pregnancy exactly, even if they have never been mated.
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Odds are that yes she is pregnant, but it's always a good idea to go in for an ultrasound after 5 weeks to confirm plus you will have an idea of how many pups she is going to have and know what to expect when she whelps.

The restlessness could be because of her body changing but I would still like to see her seen to by a vet just to make sure, would hate for there to be something wrong and us tell you just to wait it out.

I agree. Good idea to see the vet. She is uncomfortable for a reason you may not be able to visibly see. Take her in, you'll be glad you did.