We propose a new method of automatically extracting learner errors from parallel English as a Second Language (ESL) sentences in an effort to regularise annotation formats and reduce inconsistencies. Specifically, given an original and corrected sentence, our method first uses a linguistically enhanced alignment algorithm to determine the most likely mappings between tokens, and secondly employs a rule-based function to decide which alignments should be merged. Our method beats all previous approaches on the tested datasets, achieving state-of-the-art results for automatic error extraction.