There's no conflict if the Skill Level is higher than the Characteristic.
You build a dice pool as follows:
1. Look at your Skill and the relevant Characteristic.
2. The higher number is how many green ability dice you get.
3. The lower number is how many green ability dice can be upgraded into yellow Proficiency dice.
In the example you give, you would end up rolling 2 yellow dice and 1 green. This is because you would start with 3 green Ability dice (the higher number is 3), and then you would upgrade 2 of these to yellow Proficiency Dice (the lower number is 2).
I cant find an answer to this in the begginer book but here goes;
if a character has an agility of 2, rolling 2 green dice for ranged light, then adds 2 skill levels in ranged light they upgrade to 2 yellow dice. What happens if they upgrade to skill level 3 on a skill that uses an attribute of 2?