That is a very reasonable question, and Brexit is also relevant in that discussion. Perhaps it would be a good idea to require a qualified majority for cases like this.
The status quo was already established by a very qualified majority. Changing it should require a qualified majority too.
It's the same reason a thermostat is not constantly switching on and off when you cross the set temperature. Heating will start when you go a couple of degrees below the desired temperature, and it will only stop when you reach a couple of degrees more. Else, you have an unstable system (this is not my opinion, it's very basic control systems theory).