Can you point me in the direction to file an issue tracker? It's my first rodeo. The dev channel for shiny doesn't currently address the problem, but thanks for sharing.
The problem is that all plot interactivity with ggplot2 3.0 is not mapping to the data of the plot (despite specifying xvar & yvar when necessary), it's that it is reading pixels. For example, if my plot has a height of 465 pixels and I brush the lower left corner, I will get y ~ 465 regardless of what is actually in the data was in the ggplot (in this hypothetical, 0). I don't see any workaround until shiny is updated to be compatible with ggplot2 3.0.
Thanks for responding.