Playing on a Mac in windowed mode, after switching to another application, like my web browser, then back to Starmade, I am no longer able to click on anything in the UI. Also, I am no longer able to turn my ship using the mouse. I can move the mouse curser, and I can see the Starmade curser follow my mouse movements, but the ship does not turn.
As a partial workaround, opening then closing the inventory screen fixes the mouse click issue. I am now able to click on items in the ui. This does not fix the ship turning issue, however. It seems this can only be fixed by restarting the game.