Left thumb pain from using Xbox One Controller?

I was playing Call of Duty: Advanced Warfare on my Xbox One. The problem is that after some time (50 mins+), my left thumb started to hurt. I kept on playing, and even after stopping, my thumb kinda hurts now.

How do I play (or how do I use the controller) while avoid getting hurt? In the past when I used PS2 controllers there was no pain and I use my PC for countless hours and never experienced any pain. I think am just using the controller incorrectly, how do I avoid this pain?

To be honest, I really think it's a combination of overuse of your thumbs (~an hour) and the unfamiliar controller that's doing you in, causing "Gamer's Thumb". You said that you used Playstation controllers before, with no issue. Playstation controllers are a fair bit smaller, and a bit different in terms of layout compared to Xbox controllers (namely the left thumbstick and D-pad are switched).

This would probably cause discomfort after a while, as you're not as familiar with this controller as you are with a PS controller. So, like in this post, give it a break, then come back to it after a while.

I find that it is the ring around the thumb grips. On Call of Duty games, I spam the sprint button excessively, and the rim design of the controller starts to rub my thumb after a while.

I filled the hollows partly in with BluTac, that helped relieve the contact points a lot by spreading them out over a larger area.