There could be several valid reasons for the paper qualification to not match the USI Transcript. Firstly, recently completed qualifications may not have been uploaded to the national VET collections yet. This occurs quarterly for govenrment funded training and annually for fee for service training. The USI website will indicate the latest quarterly and annual data that has been uploaded.
Secondly, it could be that the student did not provide their USI for that particular training or the Training Organisation did not submit a USI with the relevant training information to the national VET collections.
Thirdly, there are a small number of RTOs, courses and individuals that are exempt from USI requirements. Some examples of training exempt from the USI are - training completed prior to 2015, national security and defence courses and single day courses completed in 2015 or 2016. For more information on USI exemptions go here.
If you have any concerns about the authenticity of the USI Transcript you should contact the relevant Training Organisation in the first instance. If you require further assistance, you can contact the USI Office by emailing USI@education.gov.au or calling 1300 857 536.