How to handle the plagiarism on references?
25% similarity is low. Similarity in references should also be discounted. I suspect it's either a mistake or something you don't have to pay attention to - you mention that your manuscript's already been accepted, and they might just be sending plagiarism reports with the acceptance email as a matter of course.

If the editor also said something like "please correct these plagiarized text", I'd write back saying that the similarities outside of the bibliography are minute, and ask for clarification.