Pamac is designed to automatically perform all updates before the installation of new software. This is intended to prevent issues that come with version mismatches, as Manjaro is a rolling distro.
As for AUR updates, they are not a very well-implemented feature. Pamac will look to the AUR to pull new updates for packages in the main repos, if the AUR is more up to date. This leads to it attempting to overwrite existing packages with new ones from the AUR, causing a bit of a mess. It is recommended to disable Pamac checking for AUR updates, and instead use a checker script.