Here are some considerations about interwiki conflicts and getting rid of them.
In an ideal case, interwiki from a X.wikipedia to Y.wikipedia should define an injective map on articles. But our world is not ideal and injectivity is often violated. Generally, it's not good to have 2 different articles in X.wikipedia having exactly the same interwiki target in Y.wikipedia. When it occurs, what should we do? Of course, one link could be just removed, but that would be vandalism, isn't it? Here are presented some schemes to get rid of conflicts without major sacrifices such as interwiki purging.
Most conflict are based on different article split-merge state in different wikipedias. Here we assume that there is a User, who is most active in wikipedia in exactly one language, say home wikipedia (H). But the User sometimes browses another languages and sees conflicting links. What are the common cases?
Outer fragmentation 
There is an article a in home wikipedia which has interwikis to many wikipedias, including article Y:a in ‘Y’ wikipedia, and versa. But ‘Y’ contains another article Y:b which also links to a.
What to do: If User knows more appropriate match in home language for Y:b, which does not have an Y:-interwiki already, the H-interwiki on Y:b should be changed to H:b. But generally, User should do nothing, because it is a problem of ‘Y’ wikipedia.
Outer confusion 
There are two articles a and b in home wikipedia which have Y-interwiki both to Y:a. This indicates incorrect interwiki data in H, but generally not a disorder.
What to do: If one of the links to Y:a is erroneous (connects two totally distinct notions), it should be removed or replaced. But if both are generally adequate, we could target a link from narrower notion in H to an anchor (Y:a#Section — see # on the picture).
There is an opinion that #-interwiki are harmful because bots do not understand them. On the other hand, bots simply ignore these useless links. Nevertheless, these links are useful for readers as much as normal interwiki links.
Home fragmentation 
There are two articles a and b in home wikipedia which have the same interwiki to many foreign wikipedias. Not necessary the same set of interwiki, but for any foreign Z to which exist links both from a and b, that Z:-interwiki should be identical.
This case is a severe home disorder (see red triangle in the center bottom of the picture) and generally is an indication to merging a and b (see right-pointing fat red arrow). But if merging is not appropriate, User should carefully replace interwiki.
Home confusion 
There is some article a, connected by interwiki with many another wikipedias. But there exist another interwiki-linked cluster b in foreign wikipedias, which links to H:a. This is the most nasty case and should be fixed as soon as possible.
What to do: Probably, the link from b to a is erroneous — remove it from all articles in the cluster b in that case. But if this link is correct, User can create a page b (in home wikipedia) containing interwiki to the cluster b, but redirecting to a. If the title of b in home wikipedia match the foreign cluster b closer, this will eventually help future splitting the article H:a to H:a and H:b. But interwiki from b will immediately stop confusing bots.
Interwiki errors 
Errors are very special case of interwiki conflicts, when interwiki-links are not just structurally confused, but semantically invalid. An example of an error is placing to the article pl:Błąd (film) a link to sq:Gabimi, where the latter is not a film, but a common name. Ironically, these words mean error. This link resulted in bot-driven contamination of en:Error (and linked articles in other languages) by links to Polish article about a film. Errors, though are amplified by interwiki bots, in almost all cases have origins in human mistakes. Errors may have following causes:
- Incorrectly added interwiki-link (as in the example above);
- Inaccurately merged articles;
- Renamed page, and a redirect quickly replaced by an article with another interwikis («Nat» case).
The remedy is always to purge (manually or by bots) all incorrect links. If a bot defends incorrect links, contact the bot owner.
See also 
- A newer look at the interlanguage link
- Fine interwiki (an innovative semantic proposal)
- Tips for resolving interwiki conflicts
- Interwiki synchronization - a page for discussing complicated cases of interwiki conflicts
- Interwiki graphs
- Wikidata - a database for centralized storage of interwiki links and other multi-language data