Including a segment of constructive criticism of another paper in my manuscript
If you make choices that only make sense if the article contains mistakes, then point out those mistakes to justify your choices. Then it becomes a matter of necessity to point out the mistakes, not one of nitpicking.
However as a matter of courtesy and due diligence, you could contact the original authors to ask them about the mistakes. Be sure to approach the subject gently. Along the lines of: "in the article you state that A was the cause of the performance gain, but in my tests I found the performance gain in C. As you see in these results.  Do you know what I did differently than you?"