I did not notice this until a few days ago I had a flat tire and when I changed the tire I found both front wheels were very hot. I wonder if this caused the flat tire. What could be the cause of the high temperature? A warped rotor or something else?

 

The wheels get pretty darn hot in normal use due to the brakes. But it if was very very hot (like it burned your hand) you may have a sticking brake caliper.

 

Brakes most likely are causing this. Though have you had your disc's replaced in awhile? Meaning, when the disc's get thinner and thinner they dissipate heat less. I know when I skinned my disc's (to do a brake job) below tolerances on another nissan, I found my wheels getting hotter than they used to. How thin have your disc's gotten?