Three flex markers are added: at the clicked position, on the previous transient marker, and on the following transient marker.
You are compressing or expanding the audio material between the middle flex marker and the other two.
Make a selection in the region with the Marquee tool, then drag the selection using the Flex tool.
Four flex markers are added: two at the marquee borders and two outside the marquee selection, at the previous and next transient markers.
You can edit the time position of the audio material between the first and second flex markers or between the third and fourth flex markers. Nothing happens to the audio material between the second and third flex markers.