1.) The ICE cube only programs at 3.3V, therefore lower voltage designs may not be compatible with this.
2.) The ICE cube has limited ability to supply current to the target emulated. Although it can supply up to 250mA of current, the voltage when supplying that current maybe much lower than desired.
3.) The emulator cannot be used for a system that uses an external CPU clock. Invalid Memory References (IMRs) will occur in PSoC Designer, due to loss of sync between the enCoRe II and the ICE cube.
4.) It is advised to run the emulator at a clock frequency of 12MHz or lower, there are some limitations to running the emulator at 24MHz, most of which are voltage related.