It's been awhile since you posted your question but in case you're still having trouble:
make sure you do not have "Real Dial Size" on. If "Real Dial Size" is on then all the layers will cut at whatever size you have your cricut set for. When it is turned off all the layers will cut so that they layer properly.
I have the Mickey & Friends cartridge, so if you need further help, let me know which image you are trying to cut and I can try it out on mine and try to help you more.