The 2 MOs in M148 are intentional in vanilla X3AP and are perfectly normal.
The 2 Jonferco HQs in Belt of Aguilar are not - unless you built one of them there yourself after a recent plot. There should be an Argon Trading Station there though.
I can only suggest that you verify your game installations (
FAQ) but the bad news is that any incorrect stations will be permanently embedded in any saves you made since an incorrect one was spawned.
I cannot say one way or the other whether any 'vanilla-safe' 3rd party script could possibly have introduced an issue into one of the vanilla plots.
A dog has a master; a cat has domestic staff.