Is this a case of data manipulation? What should I do if this is the case?
To address one of your points:


  How did they craft the input if they hadn't known the program prior to that study? By their own words, this is the most significant threat to validity. So the conclusion is this is not a valid method?


They said "Prior to the Study" - meaning before this research began. Essentially, that they weren't using a set of fixed tools that they had on hand (and thus could presumably design something to be specifically robust to). That meant they went out and found something new - and then used it. Using it can include things like crafting the input.

Your other objections are in the realm of "Do I think this is a good paper or not?" not research misconduct or data manipulation.