This problem can be fixed by adding the background-color: initial rule to the pie chart divs which represent sectors.

Open devtools on https://en.wikipedia.org/api/rest_v1/page/mobile-html/Template:Pie_chart?theme=dark and run in console:
document.querySelectorAll('.PieChartTemplate > .thumbinner > div > div').forEach(elem => elem.style.backgroundColor = "initial")

@MSantos , @Jgiannelos

Something like that can also work as a selector just to simplify things:

.PieChartTemplate div.notheme

I think its in the spectrum of dark theme issues that should be fixed in the template first. In case this is not feasible we can patch it with a workaround.

@Elitre what's the best way to reach out to the Template Editors?

I applied the suggested fix to the template. Based on testing the issue appears fixed, but there is some mobile caching so it's not correct everywhere yet.

For future reference: template editors can be notified by leaving this template on the talk page of the template in question: https://en.wikipedia.org/wiki/Template:Edit_template-protected