Foundational ontologies can be used to enable semantic interoperability in modern information systems. Aligning a domain ontology to a foundational ontology is perceived difficult, however. Reasons include confusing underlying concepts, understanding the philosophical ideologies of foundational ontologies, and lack of alignment guidance. For BFO, there is a BFO Classifier tool for alignment, but users still face challenges. To uncover some of these user challenges, an experiment was performed using 10 BFO-aligned domain ontologies. The alignment of domain entities were analysed, revealing seven different types of mistakes in the alignments. To avoid them, the BFO classifier tool was altered to improve the questions and explanations for the core principles of BFO. Thereafter, the BFO classifier tool was evaluated to measure the effect on alignment with a use-case based approach, using the GORO and AWO ontologies. The evaluation revealed that alterations facilitated alignment, as users felt more confident in their results given the improved understanding of the questions and possible answers.