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Ok so for everyone to know. I have both cbsa records and gcms notes. My gcms notes contain travel records, and presence is calculated based on EXITS only, not entry.

I’m missing many exit entries so my physical presence is calculated at 781 in the notes, even though I’m sure I have 1096.
This is repetitive but: that is clearly some type of automated calculation. That may kick you out of the quicker (AI or risk-based?) simplified approval, but it doesn't mean it will be refused or subject to extra-super-slow processing.

It almost certainly means it's kicked out to 'meat space' - a human will evaluate. They know enough to understand that a file that has many missing exits (and too many 'unmatched' entries) ... simply has missing info (the exits).

They'll work to clarify that - from some combination of your info, asking for more info, making conclusions based on other supporting evidence (work/study and tax records etc), info in your profile, etc.

Remember: they processed citizenship apps based on physical presence before they had entry/exit records like they do now. They know how to do this.

Draw your own conclusions on what to do next, of course.