One reason can be that you do not understand how to correctly calculate the amount of work experience, and which of that experience qualifies.
To enter the data into the tool, you must do the sums yourself.
When you create your EE profile, you enter the dates of your work experience and the myCIC backend does the calculation for you.
This is usually the biggest source of discrepancy.
In general, as istari alluded to, if you don't make a mistake, the score will be the same.