Sorry if this theory has been brought up, or even debunked already, but...
What if the UA shell was originally designed to contain the Barnacles within the Merope system? Maybe the Barnacles are some sort of biotech or nanotech infection, which was detected by aliens (or someone else), some time in the past, who then acted to halt its spread by constructing the UA shell.
If that's correct then it makes sense that the efficacy of the "containment field" has now been degraded by human Commanders suddenly removing large numbers of UAs from the Shell.
Now that the Shell has been degraded so much, the Barnacles are spreading rapidly out from Merope, first to other systems in the Pleiades, and now spreading to other nebulae...
In this theory the reason the UAs don't re-align to point at other infection zones, is that their designers never expected UAs to ever be interfered with out in deep space, and so never accounted for unintended sabotage of the containment mechanism.
Hopefully "They" will notice and return to fix / make more containment shells, before the Galaxy is overrun with Barnacles!