Why does it take longer if you microwave something twice than if you microwave it once?

It cools off in the interval.

Try laying a damp paper towel or other light, loose covering over the mug to prevent splattering. Stirring midway is still a good idea.

I always place a saucer over a bowl or mug of soup before microwaving it.

At work we use plastic wrap to prevent splattering. May help?

Although we are cooking food not soap.

I think it may have to do with the weird way heat builds up via microwave, that makes the constant input even more significant than it would be compared to doing the same thing in a conventional oven, but that’s just a guess.

Because it takes twice as long to microwave it twice.

If you microwave it once, some areas are hot enough and some areas are not. To get everything as hot as microwaving twice, you have to microwave it again after stirring.