I see! And considering your IELTS score, even if they dropped your work experience to 2 years, you would be still getting 13 points under this criteria. The points difference between the application and agent's review would be 12 points only. You would still have a total of 460 CRS points, more than the 459 required by the draw.Unfortunately no, the other notes are about R10 and criminality. The only possible causes of 25 points difference I can find according to CRS criteria are education and work experience based on whether I get CLB 9. My IELTS scores are R9 L8.5 W7 S7 so perfectly in line with CLB 9 standard. Also, I did not claim any additional points like siblings or arranged job in my application.
It could be education criteria like you said, but then I believe it would appear somewhere in the report, which leads us back to work experience.
I hope this is just a mistake of calculation on their part and that it can be solved soon.