Some how I have cryptsetup-nested-cryptkey in my system, but it does not exist in the main manjaro repos or the AUR. It was preventing me from updating.
Here is the problem I was getting:
resolving dependencies...
looking for conflicting packages...
:: mkinitcpio and cryptsetup-nested-cryptkey are in conflict (cryptsetup). Remove cryptsetup-nested-cryptkey? [y/N]
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: mkinitcpio and cryptsetup-nested-cryptkey are in conflict (cryptsetup<2.7.0-3)
After some investigating I have managed to get it to work using:
sudo pacman -Sy mkinitcpio cryptsetup systemd mdadm lvm2
and answering yes to remove cryptsetup-nested-cryptkey.
I was then able to update using:
sudo pacman -Syu --noconfirm
I started topic because I was looking for help, but ended up solving it myself, so I shared it in case anyone else has the same problem.