You can emulate a PC perfectly. But in practice there's a tradeoff between perfect emulation and performance, and since a VM's goal is typically to run cooperative software quickly, they aim for performance.

For example, for best performance you want to run the instructions in the VM directly on the hardware CPU so that they run as fast as they would outside the VM. But not all instructions can be run safely this way, so the VM will trap some and emulate them. This is necessarily slower, so a program can detect the presence of a VM by noticing that some instructions are much slower than they ought to be. You can lie about the time, but the bookkeeping needed to do so accurately imposes a lot of overhead.