It doesn't happen to everyone and it seems to be avoided by consuming about 50 g carbs per day.
When you go very low carb (VLC), your body tries to maintain blood sugar levels through the glycogen stored in your liver. Eventually your body switches over to ketones for fuel, reducing the need for glucose. However, not everything in your body can run on ketones, so some glucose is still necessary (about 50 g /day). If you aren't eating carbs that glucose has to come primarily from converting protein to glucose (gluconeogenesis).
Gluconeogenesis isn't very efficient, though, and it takes about 2g of protein for 1g of glucose. If you aren't getting enough protein or exercising too hard (like long distance running or biking) you can end up in a state of permanently depleted liver glycogen, which is a sign of starvation to the body. The body reacts to this by slowing the metabolism (through the thyroid).
Refeeds and diet breaks work because they replenish the liver glycogen, signalling the thyroid that everything is fine and you aren't starving. Also, I think some people are just better at gluconeogenesis and can keep their glycogen topped off.
BTW, if you do LC below 50g/day, you need to increase your protein intake quite a bit to avoid losing muscle while trying to maintain blood sugar levels.