Or implying one agent read the support letter from the university and the other could not give a damn.
OP's "travel support letter" was from a COLLEGE, not from a publicly-funded university.
Most public universities are refusing to give such a letter, saying the "student's presence in Canada is essential even if s/he has online classes". I'm not getting such a letter from my public university, and know several others who are also not getting the letter from their university.
They say if classes are ONLINE, then, we are supposed to study remotely from home & that our travel & entry is NOT ESSENTIAL currently for the fall term.
Giving such a "travel support letter" is actually against IRCC's rules of barring "non-essential" entry. OP has online classes for the fall & needs to attend synchronized sessions - meaning "real-time" classes, but online nevertheless. This makes it fully possible to study remotely from home, thereby making entry into Canada ( for studying online courses ) NON-ESSENTIAL.
I have proof that many COLLEGES are giving falsified "travel support letters", that wrongly state that the student's presence in Canada is essential, when, in fact, it is not so.
One just needs to look through this forum to see that students get such fake letters from colleges and gain entry into Canada, because they get lucky to be let in by the border officer they encounter.
All this is in direct contravention of the regulation to NOT ALLOW non-essential entry into Canada. Unfortunately, such fake support letters from colleges have facilitated the entry of many, many international students from different countries into Canada since mid-late June.
IRCC should put up clearly on their website that "online classes are non-essential", & should also issue clear guidelines to the CBSA to prevent anybody with online classes from entering. This rule of "discretion" of the officer is creating a lot of inconsistency & gaps, making it unfair for those who're not allowed to board a flight from their home country due to online classes being "non-essential".
Discretion of the officer applies during normal times, when the officer has to apply the relevant guidelines to judge whether someone could be allowed entry. Now, the guidelines themselves are all over the place; "discretion" of the officer now only means confusion, and entry into Canada is being allowed despite such entry being "non-essential" & against the rules, like the OP's wife (online classes with no "physical" lab component that can't be done remotely online, I presume).
I hope IRCC & the CBSA work asap to fix this inconsistency in their operations.
Allowing some in & some deported with exactly the same documents is something I've been hearing a lot nowadays on Twitter as well!