When you want to upgrade a certain room, or build one, you can benefit from a free build / upgrade bonus if that room will take less than 10 minutes until completely upgraded / built. So basically any room that has 9:59 left to fully upgrade, you can tap on the button which lets you upgrade it for free to benefit from a free upgrade. So make sure that you pay attention to this, and if you start making an upgrade which takes twelve minutes for example, you wait out two minutes and then benefit from the free upgrade! It's the easiest (and cheapest) way to go about making upgrades in this game.