No offense, but what do wheels have to do with pens?
I wouldn't have said anything to my 3 year old, I would have walked over and taken the pen and said, "Thank you. We will put this away now".
If he cried...so what.
There is a time and place for crayons, pens, sharpies....
We draw, write, paint on PAPER.
ONLY.
I had a neighbor who got so frustrated because her little cherub drew all over all the walls he could reach.
Why could the kid get his hands on pens and crayons?
Repeatedly?
It's not rocket science.
Don't let your child get a hold of pens and teach him that he can draw on paper and make pretty pictures for you while you are having an observed activity.
All parents have likely had a kid draw on something they shouldn't so it's not the end of the world. I just don't think at his young age he will put a correlation between writing on the carpet and not playing with toys that have wheels.
It's like telling a child, "Don't you dare touch that phone!"
It's like a moth to a flame.
Just take the object away before they have a chance.
Best wishes.