I think the explanation for 2 sets of probes would be they're specialised.
First you conduct wide-area, low-res reconnaissance to find likely places to search more in depth, with the unknown artefact. Then, when the results are in, look in more depth at likely candidates.
Granted, however, there is something a bit asymmetrical about it - if the UA can scan ships, then why do you need another probe that doesn't.
Unless the first probes/artefacts *didn't* find anything, because they were searching deep space, and what they're after isn't there, and now they're waiting for the probes to turn up something on a planet.
Perhaps.
I don't know how much we can rely on the names of the objects, "artefact" doesn't tell us much, though it acts like a probe so there would seem to be a clash. They also tried renaming the UAs at one point (Unknown Extraterrestrial Object or something like that?) but it never took.
If they both come from the same source, I think the above is likely. The UAs form a perimeter around Merope and scan everything that passes through (repairing themselves as necessary by drawing materials from the environment/container) and transmitting the findings to someone/something. Given that the probes respond to scans with energy emissions of some sort, it's possible their purpose is communication.
After that, I guess a lot depends on whether you think they came from, or are going to Merope. If they came from Merope, they're unlikely to be searching for Barnacles - so perhaps more likely they're searching for ships/civilisations, and the UPs are meant for us, and the perimeter could ultimately be to keep us out.
If they are going to Merope, they were looking for the barnacles, the probe could be meant for them, and the perimeter could be to keep us away from the barnacles, or to keep whatever's inside in.
Given the meta-alloys seem to satiate the UAs need for 'regenerative materials', perhaps the latter is more likely. They're looking for sources of meta-alloys and the UAs are to detect anything (us) intruding on them / establishing a beachhead.
-- un-substantiable theory #2387234