I just changed my pads and rotor and when I drive back home notice my passenger side have the brown mark on the rotor. My driver side doesn't have that. Is the passenger side a defective rotor or its normal on new two piece rotor? I never have brown marks on bew rotor before. Any help?

 

I think you might have glazed your rotors. Did you brake them in correctly? Smooth and slow stops for at least the first 100 miles. Never do hard braking until they're fully bedded in.

You might have to get them resurfaced.

 

Or you can try sanding the rotor surfaces yoursellf but risk creating high and low spots if not done properly

 

Maybe something got lodged between the brake pad and rotor?

 

Wat is the brown stuff?

 

Were your rotors coated? Many of them have a coating that rubs off during the first few hundred miles.

Or did that wheel get wet? Could just be a little surface rust.

 

Echoing what DaGr8GatsB suggested; it looks like glaze and so make sure that you don't brake hard during the first 100-500 brake miles. Follow the break-in procedure and all the way through the duration as specified (100-500 brake miles) without any hard braking. Do not sand the rotors, a lathe machine cuts/turns the rotors in a manner that is more precise than sanding.
There is a small chance that there is some coating on the rotors, sometimes it's cosmoline to protect the rotors from rusting when sitting on the shelves or other treatments. It'll eventually wear off within 100 brake miles.
Feel the surface and see if there is any unevenness. If there are none, go through the break-in procedure, you can find this online with varying degree of speed and duration, and then examine the rotors again. Report back with anything usual. Hope this helps.

 

After a downpour of rain, I noticed my rotors had rust marks shaped like beads of water. They properly disappeared after braking.

 

K just for a follow up my front rotor is now back to silver color but the rear brake is brownish color any1 can confirm their rear rotor is like this? The rear brake didn't get changed since it still got meat in it.