Without reviewing the entirety of the application and presence calculation, it is very difficult to guess what the problem is. Of course this is NOT a proper venue for sharing that level of information, so it is NOT likely anyone here (including me) can offer a dependable opinion about what the problem is.
As others have done above, we can do some shooting-in-the-dark and guess.
One possible target-issue not addressed so far is how item 9.b) was completed, including the information entered in the chart for temporary status.
While presence in Canada pursuant to valid visitor status counts (half day credits for days present during the eligibility period), it is nonetheless the applicant's burden to prove PRESENCE AND STATUS. Again, I cannot discern for sure what the problem is, but there is NO credit for presence UNLESS the applicant documents status. My guess is that the problem is about establishing status (as a prerequisite to counting days present) . . . otherwise it would be the kind of case in which there is RQ-related processing rather than the application being returned based on a failure to meet the presence requirement on its face.
One problem is that a super-visa, as I understand it (with the caveat I do not follow these visitor visas at all closely) authorizes a FN to enter Canada, but in itself it is NOT a grant of status in Canada . . . the individual with a super-visa must apply for entry at a PoE and then status to actually be in Canada is granted by a border officer. Documenting the latter may be the issue or related to the issue. And of course the chart in item 9.b) needs to show specific dates when visitor status was granted and expired . . . my impression is that if the super-visa dates were entered in the chart, that would NOT work. (Caveat: I am far from sure about how this works.)
There is an ill-advised tendency to equate what technically can be counted with what will actually, practically count. I have oft cautioned prospective applicants that relying on pre-landing visitor time has RISKS and can be tricky. This does NOT directly explain the issue in this case. Again, I do not know.
If IRCC is wrong, there is legal recourse. But as is the case generally, pursuing judicial remedies tends to be expensive, time-consuming, and to take a rather long time. Like pursuing any civil remedy in the courts (obtaining compensation for a personal injury, for example, can take years).
Thus, for example, the application can be re-submitted together with a formal demand that it be processed and decided on its merits, and if IRCC again returns it, then an application might be made to a Federal Court asking for a Writ of Mandamus to order IRCC to process the application. I cannot guess the probability of success. I can predict a very low probability unless this is handled by a lawyer (this judicial procedure is tricky enough for lawyers), and that for a lawyer to do this it will be very expensive, and still have no guarantee of success. But if successful, IRCC could be ordered to process the application . . . and possibly that could happen by the end of 2019 or so.
In contrast, as long as she stays in Canada another six months, she will be eligible to apply based on presence after landing, no credit for visitor time necessary. This is likely to be an available course to follow many months before obtaining relief from the Federal Court, and moreover such an application is more likely to proceed through the process faster.
