This might happen if you are executing code inside an R Markdown document, where it's possible to have the results of running code chunks displayed "inline" (right below the chunk, in the Source pane).
If you're executing code in a plain .R script file, then plots will appear in the Plots pane. If you want to see plots from your R Markdown document appear in the Plots pane, you can temporarily turn off inline results:

Look for the gear menu (next to the Knit button), and change from "Chunk Output Inline" to "Chunk Output in Console".