Your image is getting cropped just in the source pane or in the knitted document as well?
I believe that what you see on the source pane is just a place holder (or a preview) for your image before it gets knitted to its final output, so maybe this behavior is by design.
I haven't tried to knit the document. I do intend to present it within Rmarkdown like this at the moment just given the big bits of data I want preloaded and issues with some of the outputs to knit. I'll have a check.