Hey Chris,
I've had this issue too and it's too annoying.
What I did is i opened up the surface pro and heat sink removed the old dry thermal paste and applied new one, a lot of it. Then at the bottom of the screen you'll see the centre chip type thing that is in front of the keyboard connector cables i applied some thermal paste to that as well. Now it works a lot cooler than before.
It have never shown any issue since.
Hope that helps.