Holonic Manufacturing Systems (HMS) constitute an application of multi-agent systems for the control of manufacturing systems. In comparison with other multi-agent based architectures, holarchies exhibit aggregation features. As a matter of fact, all the holonic reference architectures possess aggregation-based relations, and these features are even usually described as mandatory. However, practitioners trying to implement holonic control architectures are all facing the same issue: this specificity implies many software engineering difficulties. Indeed, the models are generally not specified enough and ask the developers to make a lot of hypotheses, which are the origin of inconsistencies, misbehaviours or code maintenance issues. This article is based on the most common architecture: PROSA. The objective is to illustrate the lack of specification of the model, and introduce several ways to cope with them: better specifying the classes, better specifying the relations and finally introducing some coherent development methods.