Resilience in autonomous agent systems is about having the capacity to anticipate, respond to, adapt to, and recover from adverse and dynamic conditions in complex environments. It is associated with the intelligence possessed by the agents to preserve the functionality or to minimize the impact on functionality through a transformation, reconfiguration, or expansion performed across the system. Enhancing the resilience of systems could pave way toward higher autonomy allowing them to tackle intricate dynamic problems. The state-of-the-art systems have mostly focussed on improving the redundancy of the system, adopting decentralized control architectures, and utilizing distributed sensing capabilities. While machine learning approaches for efficient distribution and allocation of skills and tasks have enhanced the potential of these systems, they are still limited when presented with dynamic environments. To move beyond the current limitations, this paper advocates incorporating counterfactual learning models for agents to enable them with the ability to predict possible future conditions and adjust their behavior. Counterfactual learning is a topic that has recently been gaining attention as a model-agnostic and post-hoc technique to improve explainability in machine learning models. Using counterfactual causality can also help gain insights into unforeseen circumstances and make inferences about the probability of desired outcomes. We propose that this can be used in agent systems as a means to guide and prepare them to cope with unanticipated environmental conditions. This supplementary support for adaptation can enable the design of more intelligent and complex autonomous agent systems to address the multifaceted characteristics of real-world problem domains.