I received a msg from MOH and provided me subsidies for HPV vaccine, after getting injection, the clinic said I am not entitled it and this is not entitled for PR. Eventually I paid all from my Medisave, why?

SMS invitations for HPV vaccination were sent out to all eligible members of the public within the specified gender and age range, and is not indicative of subsidy eligibility. 
Criteria for subsidies is listed on the landing page (book.health.gov.sg/hpv) in the information section (Who is eligible for subsidies for HPV2 vaccination and How much will it cost?) for reference. 

"Permanent Resident (PR) females aged 9 – 26 years are eligible for government subsidies only at polyclinics."

CHAS GP Clinics
"PR females aged 9 – 26 years may receive the HPV2 vaccination at CHAS GP clinics, but it is not subsidised. The vaccination costs for HPV2 may be fully paid by MediSave. Please check with the CHAS GP clinic directly on the cost of vaccination."

Polyclinics
"SC and PR females aged 18 – 26 years may receive the subsidised HPV2 vaccination at polyclinics and may use MediSave to pay the out-of-pocket payment. The subsidy is based on individual means testing. Please check with the polyclinic directly on the cost of vaccination."