A powerful feature of stabiliser error correcting codes is the fact that stabiliser measurement projects arbitrary errors to Pauli errors, greatly simplifying the physical error correction process as well as classical simulations of code performance. However, logical non-Clifford operations can map Pauli errors to non-Pauli (Clifford) errors, and while subsequent stabiliser measurements will project the Clifford errors back to Pauli errors the resulting distributions will possess additional

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... elations that depend on both the nature of the logical operation and the structure of the code. Previous work has studied these effects when applying a transversal $T$ gate to the three-dimensional colour code and shown the existence of a non-local "linking charge" phenomenon between membranes of intersecting errors. In this work we generalise these results to the case of a $CCZ$ gate in the three-dimensional surface code and find that many aspects of the problem are much more easily understood in this setting. In particular, the emergence of linking charge is a local effect rather than a non-local one. We use the relative simplicity of Clifford errors in this setting to simulate their effect on the performance of a single-shot magic state preparation process (the first such simulation to account for the full effect of these errors) and find that while they lead to an increase in the logical error rate their effect on the threshold is minimal.