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Somehow it turns out that the issue is about options. You have to define different options for each chart. I fiddled with the codepen example. Here is what I come up with:
let chartOptions1 ..... ;
let chartOptions2 .....;
let chartOptions3 .....;
....
const chart1 = new Chart(chart1Ctx, chartOptions1);
const chart2 = new Chart(chart2Ctx, chartOptions2);
const chart3 = new Chart(chart3Ctx, chartOptions3);
After defining and using different options for each chart, I was able to see appropriate tooltips for each charts. Try it and let me know the result.
Source:stackexchange.com