This occurred in 89f14eb, as a result of changing z-index: 100 to z-index: auto. However, this appears to be necessary so that adjacent elements, such as buttons, do not obscure the tooltip. I tried many things but couldn't fix the issue so far. However, it is a minor issue, and tooltips are more important at the moment.
I'll note that currently in master, I have the flex direction as row instead of column, so there are no current instances of this tooltip/element overlap occurring. But just change row to column for the button group and you'll see it.