Waypoints aren't deleted when clicking on them and holding shift. Tried at both max and min zoom. In survival, nothing happens. In creative, the player is teleported.

Also, the pin icon tooltip says "Hold shift to edit pin", which is misleading, it should say "Hold shift to place a named waypoint or change the color, placed waypoints cannot be edited but can be removed by shift clicking."

Using map_atlases-1.20-6.0.2
supplementaries 1.20-2.8.1
moonlightlib 1.20.2.10.9

So what happens when you click on the red X?

There is no red X.

~~Edit: Doesn't happen with just listed mods installed, time to go on a wild goose chase... ~~

Turns out having multiple keybindings bound to shift breaks it

are you holding shift?

so its a keybind issue?

so to check for shift the mod simply asks vanilla using some helper methods that are often used in guis, Screen.isShiftDown()
if what you are describing is not consistent to what is advertised by that mod is likely their issue

To add to this, having the Equipment Compare's keybind "Show Comparison Tooltip" to either left shift or right shoft causes the delete marker to not show up. For example, if I set that keybind to right shift, the option to delete (X) will only show up if you press left shift; it will not work for right shift.

It is almost definetely this issue: AHilyard/EquipmentCompare#31