If the comments are no longer needed in the document you should be able to delete them using the Comment tool. Regarding the elements missing from the structure tree, you might try running the document through the free PAC 2 checker - it sometimes does a better job of pointing out the location of errors - Downloading PAC 2 - Stiftung «Zugang für alle»
You are using a very old version of Acrobat. I would request you to update to the later version (Acrobat DC) and let us know if the issues still exist.
If there are, in fact, comments on a page, they exist on their own layer, and a screen reader can not interpret where/when it should be read (that's why it's flagged as being out of the structure tree).. Deleting a comment should 'fix' this issue - this is a very common issue that I have seen with my government clients.
I hope this is helpful.