"The party official said the discrepancy is due to the fact that the names of about 3,000 people who voted at 13 polling stations outside of Toronto weren’t entered into the party’s database and therefore weren’t on the list provided to campaigns the night before the vote."

How can 3,000 people who voted not be in the party's database, and therefore not be on the voters list?

As a person verifying voters at a polling station against the official voters list, if the person wasn't on the voters list, they weren't allowed to vote. Period. 

Therefore the above explanation doesn't make sense. 

Either the G&M reporter didn't report the party official's explanation accurately, or the party official provided an incorrect explanation.

Therefore, approximately 3,000 votes recorded that weren't attributable to data entry omissions, and which exceed the number of the official voters list remain unaccounted for!

The discrepancies must be accounted for to ensure the final count is accurate.