Apple warns against closing MacBooks with a camera cover installed, as it may damage the display due to the tight clearance between the display and keyboard. The company recommends using the camera indicator light to determine if the camera is active and controlling which apps can use the camera in System Preferences. Apple suggests using a camera cover that is not thicker than 0.1mm and removing it before closing the laptop to avoid damage. This warning is intended to protect users' privacy and prevent potential display damage.