I am trying to bow my head why the histogram using qplot changes when I add facet_wrap. You can find the data that I used for this example here
The factors in my facet_grid come from using cut:
library(ggplot2)
data <- read.csv("data.csv")
data$cuts <- cut(data$y, c(0, 50, 100, 500, Inf))
So now I have this:
> summary(data)
y x cuts
Min. : 10.00 Min. :0.000 (0,50] :530
1st Qu.: 20.75 1st Qu.:1.000 (50,100] :179
Median : 46.00 Median :1.000 (100,500]:258
Mean : 110.18 Mean :0.834 (500,Inf]: 33
3rd Qu.: 121.00 3rd Qu.:1.000
Max. :1526.00 Max. :1.000
If I look only at the section where cuts=="(0,50]", it looks fine .:
qplot(x, data=subset(data, cuts=="(0,50]"))

But when I add the facet grid, the y axes are wrong:
qplot(x, data=data) + facet_grid(cuts~., scales="free_y")

Note that the y-axis on the upper side is now equal to 40 and less than 450. The only line that seems correct (500,Inf].
edit: I am using ggplot 0.9.0 in R 2.14.2