I think what's happening here is that the tooltip is showing the coordinates of the geopoint aggregation grid that your 1 data point is in, and not the coordinates of that 1 point.
If you look at my tooltip, there's 355 documents in the grid at this precision level and so it's showing the coordinates of that whole grid, not the average of all those points. In fact, ours are showing the same
"lat":42.1875 because of this grid size.
As you zoom in, the grid sizes get smaller and the tooltip gets closer to your data point (and may even match it exactly).
There is a geo centroid PR being worked on that changes this behavior a bit so that these Scaled Circles would be centered on the data instead of aligned to a grid. https://github.com/elastic/kibana/issues/5464