In Zelda Ocarina of Time (OOT) with the Redux hack/patch. One patch feature is using the d-pad to trigger the musical ocarina and the boots.
Problem: when using the analog stick, pressing down on the analog stick appears to also send d-pad down which triggers the ocarina, so normal movement is impossible with the the Redux hack.
I'm using the wireless NSO N64 controller, and had the same issue with a wired GameCube controller via RaphNet adapter.
Mapped the controllers normally in the main MiSTer controller config, and also mapped normally in the N64 core config. The N64 core controller config does not ask about mapping the d-pad at all in any case, only the analog stick is mapped in the core.