Direct Alignment Algorithms (DAAs), such as Direct Preference Optimisation (DPO) and Identity Preference Optimisation (IPO), have emerged as alternatives to online Reinforcement Learning from Human Feedback (RLHF) algorithms such as Proximal Policy Optimisation (PPO) for aligning language models to human preferences, without the need for explicit reward modelling. These methods generally aim to increase the likelihood of generating better (preferred) completions while discouraging worse (non-preferred) ones, while staying close to the original model's behaviour. In this work, we explore the relationship between completion likelihood and model performance in state-of-the-art DAAs, and identify a critical issue of likelihood over-optimisation. Contrary to expectations, we find that higher likelihood of better completions and larger margins between better and worse completion likelihoods do not necessarily lead to better performance, and may even degrade it. Our analysis reveals that while higher likelihood correlates with better memorisation of factual knowledge patterns, a slightly lower completion likelihood tends to improve output diversity, thus leading to better generalisation to unseen scenarios. Moreover, we identify two key indicators that signal when over-optimised output diversity begins to harm performance: Decreasing Entropy over Top-k Tokens and Diminishing Top-k Probability Mass. Our experimental results validate that these indicators are reliable signs of declining performance under different regularisations, helping prevent over-optimisation and improve alignment with human preferences.