I have had this exact issue many times. When phase locked editing, Logic treats untouched (dashed) transient markers as flex markers (always auto-anchoring and stretching from the next transient marker to the right, but to the left it seems to make a choice). The auto anchored markers to left and right don't become white, they stay grey dashed, but they are anchored.
As grubmanus says, often if a section of audio is a bit rushed, using the upper half flex tool to stretch the whole section with one edit is often the perfect (and fastest) solution, but impossible with this behaviour.
Your workaround worked for me, thanks David. It's a real shame that you can't use the upper half (single marker) flex tool with phase locked editing. Will just have to keep zooming in/out to keep checking all the appropriate regions are still selected when flexing multiple tracks with that tool and group editing disabled, as mistakes are easy like that!