Using ggplot, I have created a dotplot with round dots. I use ggsave to export it as a .pdf, and it opens fine on Sumatra Reader, Foxit Reader and Chrome.
However, once I open the .pdf using Adobe Illustrator for some touch ups, all of the round dots turn into rectangular dots.
If you can share your code, it might help. However, I faced absolutely no problem while viewing a dotplot in Illustrator. Used the following to generate the dotplot:
library(ggplot2)
ggplot(mtcars, aes(x = mpg)) + geom_dotplot()
In the Plots viewer, I saved it as a pdf and the opened it in Illustrator (CC 2015).