edit:
The "glich" sounds to be with the EPA system. Its not clear if the problem is technical (like an ATM giving 40 for 20 requested withdrawl) or if the system did not differentiate between "crossing" and "production and importation", by design or specification. In any event, there's not much in the article that supports any forgery or false claim about the shipment's paperwork, etc. It was more that the EPA had no or poor controls. This latter case is a grey area between willful negligence (poor design of credit-issuance-proceedures) and potential fraud (unethical re-submission).
When this is investigated by the EPA OIG (http://www.epa.gov/oig/), the chronology of the fault/exploit/fraud will be investigated along with the parties involved.
This may have involved bits of inside information such as company X hires former enforcement regulator Y from government agency Z who details the precise nature of how various governmental systems work. The possible permutations of how this situation evolved are many.
From my relatively uninformed perspective, the initial read of the article gives me the impression that this is an intentionally fraudulent scheme and criminal manipulation of the government program by the companies involved. However, I clearly do not have enough information to make such a determination.
You can bet the EPA OIG and their Canadian equivalent are going to try to get to the bottom of this.