This is a question that has been raised in one form or the other several times.
While PGC overrules the CO when it comes to lower than top level geographical attributions ("states", "counties") it does not do so where the top level ("country") is concerned. In this it does seem irrelevant whether it is a mistake or deliberate wrong attribution by the CO or nonsense when it comes to geocaching.com’s view of the world.
The latter is quite erratic. Geocaching.com does not follow any particular logic when determining which entities to consider top level ("country") and which not. A lot of dependent territories (colonies etc.) get their own top level entity whithout being souverain states, but this is not true for all of them. Some countries wildely recognised do not get their own top level entry (e.g. Kosovo). Northern Ireland is again a special case as here geocaching.com uses geographical boundaries rather than political ones and considers Northern Ireland part of Ireland in contrast to UK (which in reality should be called Great Britain if geocaching.com wants to stick to its geographical definition).
Normally COs seem to be free to choose which country they assign their cache to – which, obviously, causes quite a number of problems. In the absence of a Kosovo top level entry COs in Kososvo e.g. assign their caches either to Serbia or to Albania depending on their political views. As far as Northern Ireland is concerned there are quite a number of archived caches which are in Northern Ireland but registered as UK, but as you cannot search for them on a "state" or "county" level – as PGC simply does not inlcude Northern Ireland in the relevant pull down menus for the UK – I cannot say whether there are also any active ones, as searching for all caches in the UK leads to an overflow error. What appears from random samples is that those UK caches situated in Northern Ireland did not have any geographical attribution below the top level. It might well be that reviewers for Ireland and the UK are under the obligation to check where new caches are and correct any UK attribution by the CO for newly published caches in Northern Ireland to Ireland.
Obivously, the whole situation is very unsastisfactory. I can see three ways out of this mess:
1) Ask the CO of any erroneously attributed cache to attribute it to the correct country. This has worked so far for all caches I have found where the country was wrong. However, this is a case by case approach and will not work where the CO is not active anymore. I strongly suspect it might not work for Northern Ireland either if there is either a tacit consensus amongst COs in Northern Ireland to consider their area part of Ireland or if the reviewers there enforce this decision.
2) Ask geocaching HQ to get their geography right. They do change their geographical breakdown of the world from time to time (e.g. "recent" changes of Swiss cantons, French regions, introduction of Sark as top level entity – for whatever reason), so this is not cast in iron.
3) Hope that PGC gives up their policy to blindly believe the CO’s attribution to countries and extend their approach to attribute caches by their actual geographical situation to "states" and "counties" also to the top level ("countries"), using, of course, a more systematic approach. However, so far this was considered either a marginal problem or causing too many potential problems stemming from the discrepancy which would then obviously result between geocaching.com and PGC.
Sorry that this was a rather long (and probably not very sastifactory) answer to a short question, but as I am a big fan of geographical statistics this is an issue which I am quite interested in.