The fabric softener compartment uses an over flow method to get the fabric softener out of its compartment and into the wash load. Water comes up underneath through a syphon tube and gently fills the fabric softener dispenser and causes it to over flow in its diluted state. The reason for this is that it is the most effective way for fabric softener to be diluted prior to hitting the clothes in the drum. Fabric softener has to be diluted before coming into contact with fabrics.
This is in contrast to how detergents dispensers work which simply flush the soap powder in to the drum by water being squirted on to it from above.
It is perfectly normal to have a fabric softener dispenser full of clean water after the wash cycle. Just lift and empty it out when you need to fill it with fabric softner for your next wash
Snubef, November 2007