While trying to clone a hard drive (a SSD drive in this case) I kept getting an error that stated “this disk contains mismatched gpt and mbr”.
I found the following instructions which fixed the problem for me.
Be careful with these instructions. They are messing with the partition table and you could make your system not able to boot.
From the Clonezilla command prompt (on the second screen select enter_shell).

# sudo gdisk /dev/sda
GPT fdisk (gdisk) version 0.7.2

Partition table scan:
MBR: MBR only
BSD: not present
APM: not present
GPT: present

Found valid MBR and GPT. Which do you want to use?
1 – MBR
2 – GPT
3 – Create blank GPT

Your answer: 1
Command (? for help): x

Expert command (? for help): z
About to wipe out GPT on /dev/sda. Proceed? (Y/N): y
GPT data structures destroyed! You may now partition the disk using fdisk or
other utilities.
Blank out MBR? (Y/N): n <— do NOT choose Y!
MBR is unchanged. You may need to delete an EFI GPT (0xEE) partition
with fdisk or another tool.