That's right that " maji" belong to 5/6 JI - MA class but in this class " ya" signes the plural form. Maji ( water ) has only one form and looks like - only plural form because of prefix " ma" : ma - ji. Maji ya moto, maji ya safi etc.
Maji is a class 6 (Ma) noun. The subject prefix for this class is ya, so that is what is used.
one can get crazy with lack of consequence in those answers. The form "me" sometimes in the same part of exercises is translated as "has been" or "is" plus passive form. In fact both are ok but the system does corrections sometimes like that sometimes like that which is quite frustrating. It happens with other forms in this course.