A study permit allows you to stay in Canada provided:
- You ARE enrolled and pursuing studies, full-time.
- Yoy are NOT working more than 20h per week, except during scheduled school breaks (summer, December break, etc.)
- Your study permit will expire on the date marked on the permit or 90 days after the day you complete your studies, whichever comes first.
The last point being the most important. Notice that since you completed your program (1st year) you had 90 days to leave the country. Since you were no longer a student you had no right to be in Canada or to work. The work you did in Canada during that period was illegal.
Yes, you were authorized to be in Canada provided that you were pursuing your studies, which you weren't and you were just working illegally instead.
In conclusion, YES you should be really concerned. Why? IRCC will most likely check what it is that you were doing when during that second year that you were working. Even if you don't disclose it, which would be ground for misrepresentation and be found inadmissible to Canada, they will very likely get this information from the CRA with your SIN. If you disclose it, which is what you should do, they will realize also that you violated the conditions of your study permit and will very likely end up refusing your EE application.
You MAY get away with it, but in theory, you should not.
You should have known better...