The spans are most likely cutting up the issue so it is counting it multiple times. That can be seen via the dialog. Either way I’ll see about fixing the span issue.
As for the old underlines, nothing I can do about that. Those are not an issue with my code but issue with the code on the front page of language tools.
Normally, when my serializer was working prior to last patch, when you copy the text, it would remove the styling. But the version on the language tools website has no serializer so it just sends over the styles.
What I might do is make a fork of the Paste plugin and offer an option of paste as plain text. But that would be a feature outside of languagetool plugin itself.