Not sure what's causing this, but playing on Linux Mint there's a lot of mouse input issues when doing anything interactively. It seems like it locks the mouse in the centre position, making it extremely difficult (and sometimes impossible) to make pizzas or take them out of the oven.
Looking into the issue further, if I can figure out a cause or fix then I will create a response with more information. Right now, all I know is that when making the pizzas, once I reach step two my mouse just completely stops working, and the only way to regain control is to skip all of the steps, alt-tab out and back into the game, and click the return button.