you may be dipping into your anaerobic energy pathway too often and not replenishing the used up muscle glycogen. When you go anaerobic like on a medium long hill your body is burning an inordinate amount of stored glycogen. This is because you cannot supply the oxygen your muscles need aerobically and the cells actually manufacture the oxygen. This burns a lot of stored glycogen that is very hard to replace by eating. You hit the wall. You can get away with this for a long time but when the glycogen is gone you MUST slow down to your fat burning pace which requires a lot of oxygen. You slow down significantly and it happens very suddenly. Eventually your liver will release glycogen into your blood stream and you will feel a "second wind". You really have to get trashed to have that happen.
On long rides you need to avoid going anaerobic (hard to do because you can't always feel it happening) and you need to take in calories that go to blood glycogen very quickly so as to spare stored muscle glycogen.
Of course dehydration can accelerate the loss of glycogen because blood volume drops and you go anaerobic at a lower work load. That is when the downward spiral of the "bonK" kicks in.
Conditioning plays a very large role in all of this and if you want to ride long distance you need to ride long distance and exceed your glycogen storage levels. This increases the body's ability to store glycogen.