Xariez; In some maps the enemy is not really an enemy yet until you declare them so to speak. In human areas as an example, sometimes the patrol units won't attack me and I won't attack them (and randomly they will start attacking later).
If this is your issue, then selecting your units you have to actually attack them first, and then for the rest of the map the attack in route button mostly works.
If you are already fighting them and it still doesn't work then... What I do to get around it is when the units walk past I'll re click the aggressive AI button. This usually 'resets' them to attack.
GPS51; The issue goes a step further dealing with where the enemy unit is and where your unit is.
- If I click the attack/move option and then attack a unit of archers and select an archer in the back, my army will move through the other archers (in that same unit) until it reaches that 1 archer in the back and then start fighting.
- This gets a bit worse when the enemy unit is moving. When my units encounter them on the map, they won't attack until they reach a spot (whenever it updated last) where they think they are, and then double back to attack the new spot (because it updated).
Not sure I am explaining it right, but these add up to you having to micro manage the attack system to make sure your units are actually defending themselves. It seems that the system likes to pick 1 solider, not the entire unit to attack first.