He makes the claim that Newton's Third Law is only true in the limited case of elastic collisions, giving as counter examples inelastic collisions (ball of chewing gum deforms and sticks to wall) and destructive collisions (heavy ball tears through sheet of paper). In this he seems to be focused on kinetic energy and overlooks what Newton actually claimed:
To every action there is always opposed an equal reaction; or, the mutual actions of two bodies upon each other are always equal, and directed to contrary parts
So what happens to the kinetic energy is not considered - it may be converted into potential energy (spring compression in rubber ball, converting back to kinetic energy through the subsequent opposed forces as the ball rebounds) or simply to heat as bonds shift in the chewing gum. And it only concerns the mutual actions: to the extent that the sheet of paper impeded the motion of the ball it exerted a reactive force upon it.
He also oddly cites super-elastic collisions as a counter-example, e.g. ball hits a sheet of explosive and flies freakishly high, while overlooking that Newton is describing the physics of motion of a pair of colliding bodies: adding external forces (be they chemical, electromagnetic, or whatever) just means that you're not analyzing a Newtonian interaction.
The paper also shows some lack of editing, such as numbered paragraphs out of order (page 15 + 16) and repeated sentences, which although far from fatal flaws in themselves, suggest a lack of review.