The success of supply chains is primarily dependent on the ability to integrate and coordinate the activities of the network participants, in particular, the flow processes of products, information and financial resources from the acquisition of raw materials, to the places of consumption, which (as is stressed in the literature of the subject) contributes to the creation of a competitive edge of a supply chain and its customers. The interoperability of various actors in the supply chain is based primarily on a variety of standardized processes, but more and more often also on projects. The research conducted by the authors show that the tool for merging and joint operations of supply chain entities is setting up and the maintaining the operation of? project teams therein. However, in the practice in their activity, there are many significant problems that cause disruptions in the creation, coordination and integration of their work. The aim of the article is to present these problems - while the considerations undertaken here are of literature and empirical character.