When you lose something you do not have like 1 resolve or 1 in hand to hand for example should you not have another nagetive effect since you cannot deal with the loss?
You got lucky this time. Enjoy it while it lasts!
If for example an encounter says Test Spycraft +2 and you already have 2 in spycraft do you add 4 dice to the grey one? Or are you limited at 3 dice, the max value on the characters sheet?
You add four dice. The character's base skill cannot go above the value on the sheet, but you always add the appropriate bonus (+2 in your example).