I would assume you are marking it up using BLOCKQUOTE or something though you would have to considered; if the page was linearised would the "quote" still make sense and if so then positioning will be less of an issue regarding duplication. Though obviously any major styling or awkward positioning might confuse some users regarding "content flow".
I think that I am going to go with <aside> with a HTML5 DocType.
I think that visually, they will look OK in the site. I will try to ensure that any phrase used in a call out will stand on its own as an idea or thought.
The most irritating thing I can imagine is that the duplicate sentence or phrase will turn up either a little before or after the phrase as it appears in the text.
I think if it was on a static site, I'd consider putting the content at the end of the passage and style it individually. In this case I am putting it on a Wordpress site and I want to make it available to the site owner to use with shortcodes. So I have to add a generic style which will be safe enough for any context.