As a guy who re-enters the USA about 5 to 10 times a year with such a TN visa, with SFO, SEA, local processing at YVR, and BC/WA land/sea border crossings that is a very overblown worry. The more you cross the border, the more of a 'known' person you become and the less of a probability that becomes. You can also appeal such denials, try applying again and so on.
The scariest part is when your applying for the TN visa at the border. Make sure your hiring company lawyers draft the letter properly and possibly bring proof it's a real company if it's a new startup and so on. Don't do it yourself. Don't act like your trying to commit fraud with them because your nervous, and stick to whatever your paperwork says. If it says 'computer systems analyst', your job is a computer systems analyst. Not lead CSA, just CSA. Same with 'graphic designer', 'accountant' and so on.