You can still file with this warning. The warning is just prompting you to do one final review.
If you click "Review", you will see the amounts that differ. Usually, employment income is different on QC and Federal returns due to taxable benefits. Dividend amounts are also different due to different gross up rates.
Make sure to review downloaded slips to ensure that the amounts are correct. If the information is correct, then you may go ahead and Netfile.