i there are random squares all over the world. they are usally around vines but there are some on the ground. i cannot build in any of them and they are very hard to remove. i used kelp which works on some of them but not all the time
I think you can use /repair to get rid of those
If You can place a column on the space it might disappear.
/repair is easier to use.
/repair can’t be used by regular players on a server. Not sure about mods or single player.
Placing columns over the green areas will clear up the square.
The black area may need the elevator/door trick.
Those green squares are from tulips on sky islands I believe. I’ve always placed compost below the green spot, planted a sunflower, and then removed the sunflower. Green spot should be gone after that.
I will note that columns work too