The phenomenon doesn’t sound “random” as it can be predictably mitigated, it might involve randomness on the micro level but not the macro.
You’re also describing heating water far over the boiling point. It takes as much energy to vaporize about half of a cup of water as it does just to heat four cups of water from room temperature to boiling point. Just don’t do that, don’t put the water in for much longer than it needs to be. In fact there is no reason to bring the water to boiling temperature, it will be perfectly good for steeping tea or coffee at just below boiling temp. Still concerned? Put the spoon you are going to use to stir the tea in the measuring cup. Heat on a lower power level for longer.
I don’t take any of these precautions though. I know how long it takes to heat water. Your first time using a specific microwave you could use a thermometer and heat in half minute increments, that way you know exactly how long it will take in the future because the appliance is predictable, especially for heating straight water.
Regardless of safety it just makes sense from an environmental perspective to not heat water for longer than it takes to get to the temp you need it to be at.