This article describes a methodology for the diagnosis of failures in multi-AGV (Automatic Guided Vehicles). Today, AGVs are establishing themselves in the most advanced automatic logistics solutions, providing performance and safety that cannot be achieved with handling solutions with manual forklifts. Furthermore, thanks to the application of Industry 4.0 digital technologies, very advanced tools are available to monitor the performance and diagnose faults of fleets of AGV. In particular, studies on fault diagnosis have mainly focused on (1) the diagnosis of internal components of the automatic truck and (2) the identification of failures in the functionality of the AGV in its interaction with the surrounding environment. This paper shows an approach to fault diagnosis in multi-AGVs system, considering the interaction between each single AGV and the environment, with the scope to help the user increase the system efficiency in an existing layout. The objective of the paper is to introduce and discuss a methodology to study the failure and the available recovery actions of the AGV navigation system. Moreover, the paper presents the real AGV data acquisition and processing architecture actually deployed on the factory shop floor, as well as the result from the experimental study in a real industrial environment.