Here is an example:
Scenario is a Normal male newborn that has a circumcision and Hepatitis B vaccination while in the hospital.

ICD-9 Codes
Birth, Vaccination and Circumcision coding (V30.00, V50.2/64.0, V05.3/99.59)
groups to MS-DRG 795 Normal newborn

ICD-10 Codes
If you enter the newborn and the circumcision codes
(Z41.2/0VTTXZZ) it groups as expected to MS-DRG 795 Normal newborn.

But if you add in the vaccination codes
(Z23/3E0234Z)
it groups to a much Higher relative weight MS-DRG 794 Neonate w other significant problems.

Here are the FY2012 national unadjusted rates for these:
795 $932.52 NORMAL NEWBORN
794 $6,885.22 NEONATE W OTHER SIGNIFICANT PROBLEMS

Surely, CMS does not mean to pay nearly $5K more because a vaccine was administered?