Ah yes, seeing you "IDK" actually reminded me that DK64 did have a few sound glitches, like every now and then, like once every 20 minutes or so, a sound effect would go missing for one thing or the other, or would play with a little delay. That's the biggest problem I ever encountered with a Wii U VC N64 game (well that and the F-Zero X control issues, but that got fixed in an update soon after because so many people complained about it).
Rareware games are indeed programmed in a non-conventional way on N64, they had a lot of custom microcode stuff that they were the only ones using on that system to get the best out of it. With Rareware now being wholly owned by Microsoft, they likely didn't help with debugging the emulation part of that Wii U VC release and that task fell on Nintendo alone who did not have a hand in the making of the original code. All things considered, while it's regrettable that it's not perfect, it's still a lot more reliable than other non-official emulation solutions for that specific game.