Vaccines can cause side effect especially when administered together. You cat may just be stressed from the vaccines or may be having an allergic reaction. This site has a list of different reactions that cat be caused by vaccines (http://catinfo.org/?link=vaccines). You should call your vet if you think she is having a reaction to the vaccine.
The peeing outside the litterbox may be completely unrelated. The most common health problem associated with peeing outside the litter box is a urinary infection of blockage. These are very serious in cats and she should be seen by a vet to rule this out.