I did encounter those known issues regarding the ordering of factors as mentioned by @mnel. I tried geom_path mentioned by @mnel and Matt Bannert, and it works beautifully!

for example, in df1, W, X, and Z are factors, Y is numerical. df1 is sorted by Z

ggplot(df1,aes(X,Y))+
  geom_path(alpha=0)+ # w/o this line, points are not plotted in their order in df1
  geom_jitter(aes(color=Z,fill=Z))+
  facet_wrap('W')