Some of my CPU cores will go up to 96 degrees when using iMovie. The Mac will get really loud, too. Should I be concerned?

It will also do this on other intensive applications. But, even if I exit out iMovie and nothing is running, it will randomly start churning up.

Yeah, that's why they're called CPU-intensive programs.
You can put a laptop stand or pad underneath to improve ventilation and cooling. Some models even come with extra fans to enhance the process.

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