Was the intended behaviour an extra space or for the link to wrap both words? We have discussed in the past prompting the user to fix things which we think are errors such as these, but I wouldn't necessarily want to auto-correct them.

I know for certain that <nowiki/> was never needed the way it was auto-inserted, and it was always removed; sometimes a space was needed and sometimes not. If I had to guess, it's probably much more common that an actual trail was intended such as [[dog]]s.

I'd definitely bet on NOT adding a space. If VE/Parsoid output [[dog]]<nowiki/>s and [[dog]]<nowiki/>breeds, then I as a patroler have two things to fix; if it's [[dog]]s and [[dog]]breeds, then I need to fix only the latter and I don't even notice the first one. (The examples are from English for easiness; whether it should actually be done for English is a separate question. I'd say yes, but counter-examples are welcome.)

Some day it could be made even more DWIMmy and language-specific by checking what are the typical trails in each language. That's one of the reasons I sent this email earlier today: https://lists.wikimedia.org/pipermail/wiki-research-l/2016-July/005312.html . But that's just a big future idea.

Assuming it's related:

Wiktionary uses constructions like [[super]]<nowiki/>fluous to link to parts of the concatenated word. Obviously German language might be the biggest producer of such constructions.

In any case, the trailing magic is bad by design and should be annihilated in favour of regular [[dog|dogs]] links.

In T141689#2551684, @Danny_B wrote:

Assuming it's related:

It is!

Wiktionary uses constructions like [[super]]<nowiki/>fluous to link to parts of the concatenated word. Obviously German language might be the biggest producer of such constructions.

Thanks for the example.

Does this happen in projects other than Wiktionary?

In T141689#2551686, @Danny_B wrote:

In any case, the trailing magic is bad by design and should be annihilated in favour of regular [[dog|dogs]] links.

I agree, and I support it myself, but I'm trying to be practical, and I've got a hunch that annihilating it would be far more controversial than the original suggestion of this task, at least until a clear majority of edits are done with Visual Editor. Last time I checked it's not even 25% in any project, although it's growing.

More to the point, using [[super]]<nowiki/>fluous is a relevant example, and if it's common, there should be a different way to mark it up and not <nowiki/>, which feels like a hack.

In T141689#2551694, @Amire80 wrote:

Does this happen in projects other than Wiktionary?

I can imagine Wikipedia using it for describing origins of various proper names for instance, but admitting having no real example handy.
Same reasons for Wikivoyage, Wikibooks, and Wikiversity. (The latter two might use it for apelatives too considering some language-oriented book/course.)
Can't think of reasonable example on Wikisource, Wikiquote and Wikinews (which doesn't imply though they don't exist).

More to the point, using [[super]]<nowiki/>fluous is a relevant example, and if it's common, there should be a different way to mark it up and not <nowiki/>, which feels like a hack.

Like the <nowiki/> is hack on trailing "magic", everything similar would be the same - hack on trailing "magic"... ;-)
I can't imagine any comfortable construction though. Inserting ZWS or ZWNJ or any such hacks is inacceptable.
And introducing new syntax would be rejected for 99.9% probability.

(And VE inserting of <nowiki/> is new "magic". Again, bad by design (like majority of "magics" used in MW).)