This happens all the time on my wife's M3 MBA and the previous 2020 i7 MBA. I've been trying to figure out a solution (which is usually not to use Safari) because this happens a lot. I only realized just today that it only affects parts lower on the screen, and can be fixed so long as you are able to scroll or move the window up high enough for the element you're trying to click to be accessible in the "clickable" region. It's not always possible to do that, we hit a payment portal this morning that refused any sort of resizing, the web dialog became hidden if you tried to shrink the window, and even rescaling the display didn't allow us to get the element high enough to click. This has happened for at least the last two macOS revisions (current is macOS 27). I would love to know if you found a solution to this.