I started getting these while on 6MP years ago and do still get them while on Methotrexate (instead of 6MP, just started taking it almost a month ago).
From research that I've done is that the spots themselves are completely harmless but they could be Angioma (can be tiny and flush with the skin or be similar to a mole the puffs out and is larger) which is caused by a damaged liver (could be enlarged or fatty etc).
http://www.ehow.com/about_5831766_red-spots-caused-liver-enlargement.html So be sure to have regular blood work done to check your liver function
once a month (at
least) while on certain medications like 6MP, Imuran, Methotrexate etc.
I had an ultrasound done on my bladder for something completely different but while they were looking for that they noticed that I had a slightly fatty liver. I'm about to have blood work again to check my liver and if the numbers aren't high then my GP wants to do an ultrasound of my liver just to be sure its ok.
Keep up with your blood work and let your doctor know that you are seeing pinpoint red spots on your body (many medications say to inform your doctor if you have them, with Methotrexate its listed as a rare side effect
http://ibdcrohns.about.com/od/immunosuppressants/p/Methotrexate-Side-Effects.htm).