ggplotly breaks a discrete axis with facet_yyyy when there is only one category present in a panel, except for the case that this happens to be the first panel. I stumbled over this bug based on a question on Stackoverflow:

library(plotly)

d <- data.frame(cat = c("A", "A", "A"), pan = paste("Panel", c(1, 2, 2)))
ggplot(d, aes(cat)) +
  geom_bar() +
  facet_wrap(~pan)

ggplotly()

^{Created on 2020-06-02 by the reprex package (v0.3.0)}