Well, I would say the things to check are:
1) Double check that you uploaded the right file (you can check the file name)
2) Check the spelling of your name, reference to identity document.
3) Confirm that you followed the country specific CIC instructions exactly (many countries have more than one type of clearance certificate - for example Vietnam has form 1 and 2, and sometimes you have extra requirements - such as some Australian provinces also require driving history for some reason)?
4) Did you upload a color scan that was unaltered?
5) Did you follow the date requirements? Off the top of my head, should be after the last day you lived there - if it's not your current residence. If it is your current residence, I think it must be less than 6 months old.
If you see no issues in the above, I think it's a good chance of human error - and you should do your best to challenge the decision.
All the best!