Pretty much any kind of non-trivial digital logic. For instance emulating a typical ARM microcontroller accurately, while technically within the realm of possibility, would require a huge amount of effort; every bus and every peripheral's functionality would have to be replicated, including hard-to-gauge details like their power consumption. Even if you have access to the HDL that was used to build the chip (which you usually don't), such a simulation will never be 100% accurate.