Just to clarify, your son's original TD could only be granted until the expiry date of your old TN, There was no error in his expiry date, it matched yours.
So just to recap
You have had 2 I-94s:
Your original one which expired in April 2014 "OLD TN"
A current one which you obtained by I-129 "CURRENT TN" (I assume you are still working for your old employer? What is its expiry date?)
And now you are requesting a new I-94 so that you can begin a new job "NEW TN"
Is this correct?
like I said, your son CANNOT file I-539 at this point, since he is out of status. He must do something before he reaches the six month mark (that is six months after his TD expiry date), or he could be barred.
That means, if you are still working for your old employer, he goes NOW and gets a new TD visa at consulate and enters on a new TD, based on your CURRENT TN. It will be good until the date on your CURRENT TN. Of course, if you leave US you would also need to get Visa based on your CURRENT TN.
OR
He waits until need to get your TN approved, and then have your son exit US and return after getting a TD visa at the consulate and then entering on TD, based on your NEW TN. It will match the expiry of your NEW TN. Again, if you go you will lalso need a new visa, but based on your NEW TN .
Most importantly You MUST NOT let his days of unlawful presence extend past 183 days, which began in april!
However I don't see any need for you apply for a new TN in Mexico. You have filed I-129, and should let that take its course. Then go to Mexico and get visa stamp at the same time as your son.