Pamac default mode of operation is to update Repository packages only
To update Repository + AUR packages at the same time there is CLI option
--aur, -a : also upgrade packages installed from AUR
Pamac GUI has 2 options that are not enabled by default
Enable AUR support and Check for updates
If Repository and AUR packages are updated at the same time, pamac is likely to offer to install an AUR package to replace a Repository package that is outdated or no longer available
(similar to other AUR helpers)
Pamac GUI users should check the package list before agreeing to update and un-check any AUR packages