When creating boxplots do not add geom point layer and jitter layer both to the plots. This will print the data points twice.
Here is an example
library(ggplot2)
x <- 1:10
df <- data.frame(x=x)
qplot(data=df, y=x, x="", geom="boxplot")
qplot(data=df, y=x, x="", geom=c("boxplot", "point"))
qplot(data=df, y=x, x="", geom=c("boxplot", "jitter"))
qplot(data=df, y=x, x="", geom=c("boxplot", "point", "jitter"))