Hmm this could be!?
Are the pages indexed, will their content be available to Google search once?
I just tested it, and yes when I start the app and instantly (while it still says loading) close the tab the report in the log looks quite similar.
If this is the case, is there anything that can be done to either help or stop the indexing (as adding a robots.txt) to offer the search engines something telling them they where there already or to know what they should index?
See also this post: Search engine optimization for Shiny app
Josh: "We do not allow crawlers to start up applications"
JCheng: "I've heard rumors that Google crawlers can fully emulate web browsers in order to get at the content of single-page apps like Shiny"