This study investigated the learning difficulties of grade 12 South African students in a national chemistry examination. A quantitative analysis of students' performance in the examination revealed there was a significant difference between student performance in questions where students needed to execute a transformation across levels of chemical representation, than in questions that demanded representation at a discrete level, with students finding it more difficult to answer questions demanding a transformation. The qualitative probe in the second phase of the study elaborated upon this finding. When students were interviewed on their incorrect responses, there was substantial evidence to suggest that they did have an understanding of the concept at the discrete levels of representation in a transformation, but found it challenging to make connections across the levels. The findings of this study have implications for classroom practice, and do raise concerns on the current status of chemistry teaching as well as the preparedness of teachers in supporting students to achieve conceptual understanding in chemistry. What was also significant was that when students were prompted to explore connections with another level, they were able to extend their understanding to that level. A scaffolding approach in which a teacher supports students by making them focus on the connections between the levels should be considered. In this regard, teachers need to engage students on the relationship between the levels of chemical representation by being explicit about the transitions being made, and prompt students in making transitions across levels. (Contains 3 tables.)