The normal flexion definition for joints is reducing the joint angle by moving two bones close to each other. For example you move your forearm toward your arm and narrow the spacing in the elbow joint.
It would help you if you thought about flexion as reducing the  joint spacing in harmony with the natural structural design of the joint.  Many of the exercise motions do not consider this simple criteria. It makes no sense and yet is common. You’ll see example of this later.
Contraction of the muscles are muscles is part of this motion. Â When we say flex your biceps, we really mean flex your elbow joint and contract your biceps. Again for health and performance reasons, it is important to think of flexion in relationship to your joints and not muscles.