This appears to have been happening for about a year and you can see a bunch of example here https://ja.wikipedia.org/w/index.php?title=%E7%89%B9%E5%88%A5:%E6%8A%95%E7%A8%BF%E8%A8%98%E9%8C%B2/Wakkie1379&offset=&limit=500&target=Wakkie1379

Content translation editing surface has been fragile when dealing with some complex elements such as references at times. We are currently working on version 2 which uses a more solid editing surface provided by VisualEditor. The new version will make dealing with references as reliable as Visual Editor.

Also the Wikipedia page " HIV/AIDS" ends up as " #sida/de VIH "

This other issue may be caused by the automatic translation service. In this case, Apertium may be providing a sub-optimal translation. In addition, since Apertium only works with plain text, Content Translaiton has to recreate the links and references in the right place, resulting on the link being applied on the wrong place in some cases. This is something we cannot do much about since it depends on external translation services.

@Pginer-WMF I translated the Atazanavir article into a draft and everything seems ok, can you double check please?

@Jpita looking at your draft and I see that a bunch of the references have gone missing.

Here every sentence has a reference https://en.wikipedia.org/wiki/Atazanavir

Here I am see at least 5 are missing https://es.wikipedia.org/wiki/Usuario:Jpita23/Atazanavir

Thanks @Doc_James , we'll put this in our todo list.

I made a sample of the problematic Wikitext in this page (quick link to translate)

The example is a reference that is used in multiple parts of a paragraph. All those instances appear in Content Translation when the paragraphs are added to the translation. But some of them are lost after publishing.

Original content:

In Content Translation:

After publishing:

The red circles show the places where the reference "[1]" was expected to appear but failed to do so.