Permatution or Combination

a) 9: Three colors for the first pen, three for the second
b) 6: If blue is first, the second can be any of the three. If green is first and you've already counted blue, you have two options. For yellow, your only option is yellow.

I think you were wrong
We choose it at the same time.

How about we choose 2 blue pens at the same times?

It doesn't matter. Since you have so few options, you can just map them out yourself if you need to prove it.

Permutations
BB
BG
BY
GB
GG
GY
YB
YG
YY

For combinations just remove the ones that form duplicates (GB, YB, YG).