The problem was solved. I followed these steps:
Reported a "Technical issue" through the website. Got no answer after 24 hours.
I called CIC today and explained the situation. They say they don't take those enquiries on the phone and I should fill an IRCC web form instead.
I withdrew my application and created a new one from scratch with the exact same information. I got the points that I was missing.
Hope this helps anyone facing a similar issue.