No, they do not stack (their penalties do, though). The fatigue track and the wounds track (so to speak) are independent.
First, there is no clear mechanism that explains how they would stack if they could. For example, a character that receives two wounds first and then a level of fatigue could be seen as three wounds and working, but a character who received a level of fatigue and then two wounds could be seen as having three levels of fatigue and thus incapacitated... but it is the same situation in a different order.
You can also look at some posts from the official forums like this one where a character has three wounds and two levels of fatigue and it is not flagged as an impossible situation by Clint Black.
So no, a fatigued or exhausted character is not incapacitated when they receive three wounds.