Agents trained via deep reinforcement learning (RL) routinely fail to generalize to unseen environments, even when these share the same underlying dynamics as the training levels. Understanding the generalization properties of RL is one of the challenges of modern machine learning. Towards this goal, we analyze policy learning in the context of Partially Observable Markov Decision Processes (POMDPs) and formalize the dynamics of training levels as instances. We prove that, independently of the exploration strategy, reusing instances introduces significant changes on the effective Markov dynamics the agent observes during training. Maximizing expected rewards impacts the learned belief state of the agent by inducing undesired instance-specific speed-running policies instead of generalizable ones, which are sub-optimal on the training set. We provide generalization bounds to the value gap in train and test environments based on the number of training instances, and use insights based on these to improve performance on unseen levels. We propose training a shared belief representation over an ensemble of specialized policies, from which we compute a consensus policy that is used for data collection, disallowing instance-specific exploitation. We experimentally validate our theory, observations, and the proposed computational solution over the CoinRun benchmark.