Hmm, that is odd indeed. I might suggest changing your preferences so that R Markdown outputs are shown in the terminal rather than inline. This can be done in Preferences.
Preferences > R Markdown > Show output inline for all R Markdown documents
If you uncheck the above it may help. You may need to reset RStudio. I also have the following option changed:
Show equation and image previous: In a popup
Both of these settings avoids cluttering my Rmd with outputs. Personal preference.