The endurance (hull integrity) of your base is defined by points. Your base will begin with 10 points of endurance and then when each new construction element is added to the structure a number of points is subtracted from integrity. Expanding your base without any strengthening elements will cause the structure to crack and start leaking.
You will not be able to simply patch the holes as new ones will appear. To prevent this from happening you will need to make sure the integrity of your hull is above 0. If it is not you need to solve the problem by strengthening the structure of the base by using wall reinforcements or foundations. Adding these elements will add points to the hull integrity of your base. You will only be able to proceed with patching leaks with the repair tool once your base has regained positive integrity. When you then fix the leaks the base computer will inform you that the water is being drained.