I have encountered this issue as well; I've noticed that it also occurs when copying a citation from the content translation tool into the normal visual editor, so this might be a bug with the visual editor as a whole and not just with the content translation tool.

video by @Thecatcherintherye for the production of the problem:
https://streamable.com/c4kt6x

I'm informing you that the problem is the same as reported in this other task: T412486. This problem isn't just affecting translations from English to Portuguese; it's affecting other languages as well.

I believe the issue occurs when translating an article which uses {{reflist}} (or a local equivalent) instead of <references /> – presumably because ContentTranslate can't properly detect the references. I couldn't reproduce the bug in articles without such a template.

My experience is that the reference name plays a big part in this bug. All the references that have no name end up the same as the first one (the 'undefined' one). The named references are spared, they work well. It is true I only translated from the English Wikipedia, which employs the {{reflist}} template, but the ref name handling is the place to investigate, I think.