The gate agent realized exactly what this couple was doing and considered it to be bad form and violation of the unwritten rules of air travel seating courtesy. To her, splitting seats like this couple did and leaving an empty middle is an abhorrent practice, because it makes it harder for her to seat other passengers near each other (like aisle-aisle) and harder for her to accommodate other passengers' window/aisle seating preferences.

When couples do this it can lead to more passengers complaining and moaning to the gate agent about not getting seats they want.

So she torpedoed the couple's scheme and probably enjoyed doing it.