Sounds like a composer issue.
I still tease my boss when I find a computer with his user account on it for the same reason.
When using composer if you want to put something into a Users home directory you need to make it a .dmg and use the Fill Existing Users option.
If you aren't trying to put something into the users homefolder then just make sure to delete the unnecessary things out of your .pkg before building it.
Also get a test computer with a test account to try your policies on it before you push it out to all the macbooks in the school. (Or use VM's but that's more complicated and I honestly haven't put in the time to set that up myself.)
#!/bin/sh
rm -rf /Users/YOURUSERNAME