Thanks for your reply.
The reason I figure out the difference is because some work experience the documents I have do not have all the information CIC requested, e.g. I have a work certificate/employment letter, it won't list my job duties, but would only give information like title, duration, salary, these kind of information. I did not provide all these because I thought the more you gave the more mistake you could make and let CIC case officer picky on me. So I only submitted all the minimum documents to support my work history but they are all satisfying CIC's requirements.
The mistake I made is the 2nd question asked about work experience in the last 10 years after the Canada work experience in the CRS tool
http://www.cic.gc.ca/english/immigrate/skilled/crs-tool.asp, it only means foreign experience, but I interpreted as foreign+canada, so I only gave 2 years foreign for 1 job and 1 year in Canada, totally over 3 years. That is why my points decreased in the ITA application, I found out 3 months after I submitted my application.
Which I think my application would be marked as incomplete in R10 and get rejected.