Cases of virus outbreaks, though mild cases and nothing that would typically cause death, have been reported. In recent news, a local restaurant was closed because samples of the Norwalk Virus were detected at the restaurant.

Female Anopheles
A good way to gauge the cleanliness of a restaurant in Costa Rica is to immediately upon entrance of the establishment, check the restrooms to see what condition they are in.
Usually, a poorly cleaned restaurant reflects how clean the kitchen area and sanitary safety of the staff is.
Vector Borne Diseases
Malaria and Yellow Fever have been reported with isolated cases in Costa Rica, but typically are very rare and never heard of. The most prone areas for these diseases is The North Caribbean Region, where a lot of rainfall occurs annually on a consistent basis.
The water tends to pool in this area of the country making a perfect breeding ground for the mosquitoes that transmit these diseases. It is not necessary to get any vaccinations for these diseases unless you intend on going to these areas of the country for any extended period of time.