That seems weird - at least your description
As I understand you - you seem to be experiencing the updates from two different branches?
I don’t think seeing updates from two branches should be possible but alas I can figure a way.
It is possible is when you have one branch in pacman-mirrors.conf - which is the branch that pamac uses and your mirrorlist would contain the url of a different branch and as such it would be the one that pacman uses.
Branch = testing
Server = https://www.uex.dk/public/manjaro/stable/$repo/$arch
This scenario is impossible to solve as it is a user created scenario.
It can indeed be created by abusing the api of pacman-mirrors, and it would have been done so quite intentional. Which branch should be the chosen in the scenario?
The obvious solution is for users not to deliberately create the scenario in the first place.
There is no cure for - in lack of a better word - ignorance.