What does “each side counts as one” mean?

For exercises that indicate "each side counts as one repetition", when you perform the right side you count 1 repetition, then left side 2 repetitions and so on. The assigned number of repetitions equals the total number, left and right sides combined.

Example: 20 Lunges = 10 left leg + 10 right leg

Note: If you are assigned an odd number of repetitions (5, 15, 25) you can perform one more repetition to even the load on each side.

Exception: 
One Repetition of Plank Switch=
1. Start the exercise with both forearms on the ground (planking position)
2. Extend right arm up, and then extend the left arm up
3. Move right arm down and then left arm back down into planking position.

The second repetition should then begin with extending the left arm followed by the right arm.