Accepted answer

(Moving this from the comment section)

Take a look at this:

In the updateChart function you select by the circle class:

// update the circles at each data points
svg.selectAll('.circle') // here you correctly select all with the circle class
      .attr('class', 'circle all')
      .attr('cx', (d) => { return this.axis.x(d.time);})
      .attr('cy', (d) => { return this.axis.y(d.count);});

but here, on mouseover, you remove the circle class and replace it with circle--highlight:

            .attr('class', 'circle all')
            .attr('cx', (d) => { return this.axis.x(d.time);})
            .attr('cy', (d) => { return this.axis.y(d.count);})
            .attr('r', 4)
            .on('mousemove', function(d) {
              // START: Show tooltip
                .style('opacity', 1);

              div.html('<div class="date--time">'
                + d.time
                + '</div><div class="count">'  + d.count + ' incidents</div>')
                .style('left', (d3.event.pageX) + 'px')
                .style('top', (d3.event.pageY - 70) + 'px');

                .attr('r', 6)
                .attr('class', 'circle--highlight'); // here you change the class from circle all 
              // to just circle--highlight, 
              // so when you are hovering a circle and the chart changes, 
              // the circle you have hovered won't be updated because 
              // it won't be selected due to the class difference

              // END: Show tooltip
            .on('mouseleave', function() {
              // hide tooltip and return the circles to original style
               .style('opacity', 0);

              // set the circle back to normal
                .attr('r', 4)
                .attr('class', 'circle all');

So a solution would be to also add the circle class along with the circle--highlight like this:
              .attr('r', 6)
              .attr('class', 'circle circle--highlight');

Or change your select in the updateChart like this:


but that would need many more adjustments to your script in order for it to work as expected.

Hope this helps! Good luck!

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