Suggested fix (unconfirmed): Update your game to version 1.0.13 or later. If the issue persists, contact the developers via email at cheshendog@gmail.com.
Suggested fix (unconfirmed): Toggle the UI scaling option in the Gameplay section of the options menu, or switch between fullscreen and windowed display modes to adjust the layout.
Fix for players, who experience various bugs in the game, especially bugged skill tree, mutagens not being spent and corrupted save file after doing anything inside the skill tree.
Suggested fix (unconfirmed): Equip the correct tool and aim your cursor directly at the base of the tree or rock. Ensure you are using an axe for trees and a pickaxe for ores and stones.