Vasco Castela is one of those affected.
He has been teaching ethics full time in B.C. for seven years, but once his work visa runs out on Friday, his teaching days are over.
Originally from Portugal, Castela—who has a PhD in ethics and teaches at two Metro Vancouver colleges—first applied for permanent residency in 2013, but was turned down because he didn't meet the required number of working hours. He says that's because CIC failed to take into account any hours not physically spent in front of students teaching, such as prep time and marking.
Two months ago, with the expiration of his work visa approaching, Castela applied again with the correct number of hours, but his application was returned—unopened and unprocessed—because the cap on applications had been reached.
Unbeknownst to Castela, the CIC had hit its cap under the Canadian Experience Class (CEC) on Oct. 22, 2014 and did not post this information to its website. It had previously announced it would accept 8,000 applications between May 1 and Dec. 31, 2014.
As the CEC program was being terminated at that point, there was a surge of applications from people trying to get in before the new Express Entry system with new criteria launched on Jan. 1, 2015.
But the information that last year's cap had been reached in October was only made public earlier this week—more than two months after the fact.
"It's absolutely outrageous," Castel told CBC News.
His opinion is shared by Toronto immigration lawyer Michael Niren.
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"In Canada we're supposed to have what we call the rule of law and part of that means consistency and predictability and reliability," he said.
"When you change the rules of the game so quickly—and in this case without even announcing it—it's not acceptable. Applicants are basically just shooting darts hoping that they stick and it's not good."
Experts say Castela is among thousands of people now left with little hope of staying in Canada thanks to a systemic failure by government.
"They have an obligation, a procedural fairness we'll call it, to announce on a timely basis when a cap has been reached and they obviously haven't done that...There could be good grounds for a class action suit."
Castela says from the day he arrived, it was his intention was to make Canada his home, but he doesn't expect to qualify for permanent residency under the new program that went into effect this year. Still, he plans to apply for a visitor visa in an attempt to buy him a few more weeks while he explores his options.
"I am very angry," he said Friday. "I'm angry, and I'm going to say goodbye to my students today and yeah, it's going to be a very emotional time."
CBC News asked CIC to explain why it did not inform the public that its cap had been reached two months ago, but it did not provide an answer.