One of the most widely used tasks for evaluating Large Language Models (LLMs) is Multiple-Choice Question Answering (MCQA). While open-ended question answering tasks are more challenging to evaluate, MCQA tasks are, in principle, easier to assess, as the model's answer is thought to be simple to extract and is compared directly to a set of predefined choices. However, recent studies have started to question the reliability of MCQA evaluation, showing that multiple factors can significantly impact the reported performance of LLMs, especially when the model generates free-form text before selecting one of the answer choices. In this work, we shed light on the inconsistencies of MCQA evaluation strategies, which can lead to inaccurate and misleading model comparisons. We systematically analyze whether existing answer extraction methods are aligned with human judgment, and how they are influenced by answer constraints in the prompt across different domains. Our experiments demonstrate that traditional evaluation strategies often underestimate LLM capabilities, while LLM-based answer extractors are prone to systematic errors. Moreover, we reveal a fundamental trade-off between including format constraints in the prompt to simplify answer extraction and allowing models to generate free-form text to improve reasoning. Our findings call for standardized evaluation methodologies and highlight the need for more reliable and consistent MCQA evaluation practices.