I have different perspective.
It is really a matter of offence or not, and it really depends on the visa officer to determine if it is a "big concern". If i were you i wouldn't risk myself to mention the three weeks. Because different companies have different tax filing frequency, and it happens from time to time that employer files your tax late or even do a subpay for the work you did in the last period.
If i were you i would talk to my boss, if you guys get along well, explain the fact and if in the future CIC questions about he should just tell them the 3 weeks pay was just subpay from periods before or from overtime owed to you and the didn't work after that. If your relation with your boss wasn't good, i will still suggest not reporting the 3 weeks, it is only 1 and half pay period, it is not 3 months or even 1 month.
After all, the communication between cic and CRA is terrible, and CRA only has your record of your tax amount by period, i researched this a lot and i don't think CIC have very detailed information about your tax information, which would be the only lead to your work time. The decision on your CEC application is mostly determined by your reference letter, just make sure the period mentioned there is coresponding.
Good luck, bro.