bug in sdx kit?

I wanted to use sdx kit on my chrono-timer script (whose source is available on the wiki). However, it kept generating errors indicating problems with rsync not being able to delete some files.
It turns out that you can't have a dot file in a wrapped app. In other words, no ".file" or ".folder" or it will complain and error out.
I can't find more info on sdx.kit so I wonder if this is some sort of a feature or if it is indeed a bug.