No Codepen needed, also occurs in the demo at https://apexcharts.com/javascript-chart-demos/line-charts/null-values/
Hover over 7 on the x axis. The colors of the points on the yellow and blue lines are swapped.

I encountered this on a real project, and the more lines you have the weirder the behaviour of the dot colors. Sometimes, a dot color is showing twice:

The issue vanishes when setting the markers option to a value > 0.
Which version of apexcharts are you using? I cannot reproduce this with the latest version.
Latest version from npm, but as I said it also occurs in the demo (tested with Firefox latest, Windows).
Ah! I was checking in chrome.
Will test in Firefox.
I'm seeing this behavior in Chrome on Mac
It's a chart with 4 series, multiple types in use: area, line, area, column. I'd like to set markers.size: 0 to hide the line markers. But that causes the tooltip markers to display the wrong colors on hover. Based on @Connum's comment I tried setting markers.size to .001 - something greater than 0 but still not easily visible. It seems to work.
Sharing here in case it helps someone. Here's my chart setup:
series: [{
name: 'Total Members',
type: 'area',
data: [100, 100, 105, 105, 98, 98, 98, 100, 100, 100, 99, 99]
}, {
name: 'Members with Suggestions/Reconfirmations',
type: 'line',
data: [85, 85, 85, 92, 92, 92, 87, 87, 87, 90, 90, 90]
}, {
name: 'Total Risk Adjusted Members',
type: 'area',
data: [6, 22, 30, 36, 40, 46, 50, 52, 54, 60, 68, 70]
}, {
name: 'Members Risk Adjusted this Month',
type: 'column',
data: [6, 16, 8, 6, 4, 6, 4, 2, 2, 6, 8, 2]
}],
chartOptions: {
chart: {
type: 'line',
stacked: false,
},
colors: ['#A6FAEC', '#237C7C', '#FAD1C6', '#ED6542'],
stroke: {
colors: ['#A6FAEC', '#237C7C', '#ED6542', '#ED6542'],
width: [1, 3, 1, 0],
curve: ['smooth', 'smooth', 'straight']
},
fill: {
// colors: ...,
opacity: [0.4, 1, .8, 1]
},
markers: {
// setting marker size to something really small but greater than 0
// 1 to work around a bug in the tooltip marker colors
// which seems to randomly sort the marker colors
// https://github.com/apexcharts/apexcharts.js/issues/1427
size: .001, // setting to 0 triggers the bug in this chart
},
plotOptions: {
bar: {
columnWidth: '50%',
}
},
xaxis: {
categories: [
'Jan 2021', 'Feb 2021', 'Mar 2021',
'Apr 2021', 'May 2021', 'Jun 2021',
'Jul 2021', 'Aug 2021', 'Sep 2021',
'Oct 2021', 'Nov 2021', 'Dec 2021'
]
},
yaxis: {
title: {
text: 'Members',
},
min: 0,
max: 110,
tickAmount: 110/10
},
tooltip: {
shared: true,
intersect: false,
}
},