The classical objective for multiple agents evolving in the same environment is the preservation of a predefined formation because it reinforces the safety of the global system and further lightens the supervision task. One of the major issues for this objective is the task assignment problem, which can be formulated in terms of an optimization problem by employing set-theoretic methods. In real time the agents will be steered into the defined formation via task (re)allocation and classical feedback mechanisms. The task assignment calculation is often performed in an offline design stage, without considering the possible variation of the number of agents in the global system. These changes (i.e., including/excluding an agent from a formation) can be regarded as a typical fault, due to some serious damages on the components or due to the operator decision. In this context, the present chapter proposes a new algorithm for the dynamical task assignment formulation of multi-agent systems in view of real-time optimization by including fault detection and isolation capabilities. This algorithm allows to detect whether there is a fault in the global multi-agent system, to isolate the faulty agent and to integrate a recovered/healthy agent. The proposed methods will be illustrated by means of a numerical example with connections to multi-vehicle systems.