I can't reproduce your issue, but you could also make the plot manually
library(incidence)
library(outbreaks)
dat <- ebola_sim$linelist$date_of_onset
class(dat)
#> [1] "Date"
i <- incidence(dat)
plot(i)
# You can also do it manually
library(ggplot2)
dates <- data.frame(date = as.Date(i$dates),
count = i$counts)
ggplot(dates, aes(x = date, y = count)) +
geom_col() +
labs(x = "",
y = "Daily incidence")