Yes - we've definitely seen that. The most common thing we've see if that you start with a jenkins job that just runs a build process, and then you end up with a jenkins job that has a huge shell script which calls the build process somewhere in the middle, that's unversioned.

To resolve that we've tried to push the shell script into a file in the repository, which Jenkins then checks out and runs, which makes it easier to maintain and faster to set up new build machines.