But that is to be expected, right? Sprint requires different metabolic rate and muscle specialization than marathon or even 400m run. Even the legs are visibly different. They train for a specific distance, no more and no less. Since it is a common occurrence for them to train on said distance, they get more and more specialized. Sprint requires fast-twitch muscle fibers that offer tremendous boost for a short time, others require slow-twitch fibers that can sustain constant work for a long time. Since they train exclusively one type, it's not unreasonable to assume that they would have problems. But they can re-adapt, for a cost of reduced specialization of muscle groups.
You can test it yourself with a bike: change your sitting height or (in case of training bikes) the resistance of the machine itself. After switching from your normal sweet-spot you will get problems and significantly will put more effort into it, but after about a month of daily workout under only this specific setting you will get better. Now change it to the old settings and you will get a repeat of the situation, only not to such degree as with the first change.
Another variant with a training bike would be to train fast-paced bursts under low-resistance for a while and then switch to long-distance and consistent-pace with an amount of calories burned being a conserved value for sake of comparison. I can actually recommend this type of training anyway, it's a great way to precisely avoid getting over-specialized.
NPR: The Physics of Olympic Bodies,
The Role of Muscle Fibers in Running.