There are several reasons why explaining the observed acceleration is so hard. The cosmological constant (the measure of how much dark energy there is) is a tiny positive number which seems to require a lot of “fine tuning” to explain theoretically. We can easily include it in general relativity, but our best understanding of quantum physics says that if it is there then it should be much larger. This means there probably is something we don’t understand about its microscopic origins. If we try to build a microscopic model that has this small constant using string theory (our best guest at a complete theory), we find that such models are hard to create. In fact, it is not clear that any model that includes dark energy is even valid in string theory! Any way we look at it, it seems more difficult to explain this number if it is tiny and positive than if it is strictly zero (no acceleration).
Finally, theoreticians don’t have much to go on when explaining this phenomenon besides this one single number — there aren’t closely related experiments we can combine to come up with a coherent picture of what’s happening. Combine this with particle physics, where accelerators provide us with an abundance of data. It is a single tiny number that has puzzled theoreticians for decades.