Cannot type the minus sign in the boxes, only digits are accepted. It should be possible for the first character to be a minus sign as long as it's followed by digits.

It's normal. These fields acceps only integer values or nothing.

Well negative values are integers too but you can't input them... That means you can never set a waypoint with negative coordinates without actually going there. Those inputs thus only allow you to set inputs for a quarter of the Minecraft world and the rest is inaccessible.

You can. Just enter any digit and type minus before it.

Ok but it's pretty ridiculous and no one expects software to work like that. It's so ridiculous that as a user I had to open a bug report to find out the workaround. :-/ At the very least put up some text so people know how to do it.

It's protection from enter wrong data to the field. And you are the first to whom it caused inconvenience.