Thanks for the bug report, I confirm it as a bug and it is now fixed in the source code repository so it will be fixed in the next release but will require rebuilding the index in the child site.
This bug has actually been reported before but I wasn't able to reproduce it the previous time(s). It turned out that is only happens when batch indexing and not when just indexing a single item and this is why I wasn't able to see it before. Batch indexing happens when you rebuild the index or when all the items for a page are re-indexed due to changes in view roles on a page, whereas item indexing happens when you update the content of a single item. When batch indexing it was including the folder segment in the url it indexed and this caused it to be duplicated since we add the folder segment when rendering the url on the search results page. Whereas when indexing a single item it was correctly not including the folder segment.
You can confirm this by finding a result for an html article that has the bad url in search results, go to the item and make a small edit, then wait a few minutes to allow time for the item to be re-indexed and you will see that if you then search for it it has the correct url.
I expect to make a new release within the next 2 weeks at latest which will have the fix.