In this paper we discuss the types of knowledge used by six middle school students as they engaged with a debugging task designed to integrate ideas from computer science, mathematics and science. Our findings show that the computational thinking practice of debugging is a rich source of opportunities to integrate these different disciplines. The analysis illustrates how the types of knowledge the students did and did not use at each step of the debugging process were related to their ability to succeed at each step. Our work contributes to theory and practice by uncovering implications for studying debugging through two refined frameworks and for designing debugging tasks to support transdisciplinary learning.