It just takes time until calcium scale starts building up inside the pipe work of a vacuum toilet system. The flow reduces and eventually the system is blocked. It is not always easy to locate, let alone solve these blockages. Getting access to the pipes often takes demolishing elements of the vessel's interior and always means downtime in the toilet system and all the additional inconvenience that results from it.
The most common solution is to avoid blockage by the periodic cleaning of the system. As this involves taking out of operation lines of toilets, it is obvious that the cure is often worse than the problem. The disconnected line may be saturated in diluted acid (which does not only disrupt the services on board, but may also cause damage by leakage) or recirculated in a closed loop, which is more effective, but may have the same negative effects.