This is related to the scales="free" bullet of #161, but is probably worth noting separately. I'll send a pull request in attempt to fix both. I've uploaded this plot to demonstrate a bug in the y-axis limits:
library("plotly")
no_panels <- ggplot(mtcars, aes(mpg, wt)) + geom_point()
no_panels + facet_wrap(~am+vs, scales = "free")
On a larger note, the package currently seems a little confused about the conceptual difference between facet_grid and facet_wrap in terms of free scales. For facet_grid, the y-axis/x-axis has to be fixed for a given row/column. But for facet_wrap, each panel is allowed to have it's own axis. I think this figure from the ggplot2 book helps demonstrate that:

@chriddyp @mkcor do you know if the plotly API would support drawing an axis on each panel?