There are a couple of reasons that Auto FTP Manager will skip a scheduled run.

If you have two different schedules associated with same Automated Transfer Profile then the second schedule will be skipped if the first one is already running.

Another example where a schedule may be skipped is if you have set a custom profile to schedule a transfer every minute, you will get a skipped message whenever the next schedule launches because the transfer is already in progress for the Automated Transfer profile.