My girlfriend recently purchased her first car.
She purchased a 2011 Kia Optima LX. The car has given her no problems the first month and half.
The car has a clean bill of health as far as I could find (CarFax and Etc.) has no visible damage.
The car was purchased from a dealership that we purchased our previous cars.

Here is where the problem arises:
Starting about a week ago there is a weird studder or like thud.
Now this thud only happens when the car is coming to a complete stop. Not when accelerating.
It feels similar to a small bump. It's not a long bump. I guess the best way to put is it feels like running over a squirrel for 1 second.
It only studders like this for the first 10 - 15 minutes of operation and then each stop after that is normal.
Both the rotors and brakes are brand new.
Nothing has changed, just her day to day driving to work. No accidents or anything.

I ask for your help to maybe lead me in the right direction.
She plans on taking it to the dealership and having them do maintenance, but i would like to have some ideas so they aren't trying to pull anything.

My Google searches came up pretty barren.

My first idea was the rotors/brakes, but they were replaced.
My second idea was related to ABS system. Like bad wiring or sensor.

Any help would be greatly appreciated.

Does the pedal get squishy when you come to a stop? Like the pedal feels like it pulses when you break?

Just asked her right now. She said it feels completely normal.
She said there is no difference from when she got the car until now.

Still could be rotors,it only takes running into a puddle of water after there hot.Ive replaced warped rotors before only to have it happen again.But if it doesn't do it all the time that's probably not it.Could be air in the lines,maybe bleed them.Would make sense if you just had a break job done.Take it back where the breaks were done.They should also be able to see if its showing a code on the abs.I'd also try putting the car in neutral before a stop to see if i got the same Effect'.That would eliminate transmission problems.I think it could be transmission related because you say it stops after 10-15 minutes of operation which would be when the transmission warmed up.If it were electrical it wouldn't stop,or it would get worse.If it were rotors it would stay the same.But still it could be the booster or air.Do i quick inspect and make sure fluid is good and the cap is on secure.If it were me id pull the wheels and check the calipers to see if they are releasing,maybe one is sticking.Does it pull to one side?

also could be ur wheel bearing going out on one side.

I went to the dealership today.
They replaced a brake switch (Factory Recall) and updated the computer system.
I doubt this will fix it. But I guess I'll see.

I checked out what you said super about going into neutral.
Turns out it does not do it while in neutral.
It doesn't pull to one side, but I'm gonna pull all the tires tomorrow and see whats going on.

Switch should fix it,makes perfect sense.Switch tells the transmission your stopping.The reason for the jerkiness was the transmission not knowing what was up when you applied the brake.Looks like you lucked out.Hope that fixed it.

I hope so. Today I didn't do it for the first time. So I'll keep my fingers crossed for tomorrow! :D