it could be that the process being executed for some external reason is taking longer to complete, if cron starts the same app again without the first instance stopping, and the second trying to do the same stuff with the same data, (repead this a few times) you could run into issues
for example: i have a script that filters my mail on a imap account as i use clients on many different computers. when the script is started before the other is stopped, they will conflict and lock eachother out - neither will complete... then cron starts the next one etc.
the size of emails on the imap account in my case could cause such issues (at least used to be able to cause the issues).
that is the only thing i could think of (external reason for time consuption, not enough time for process to complete)
Edit: oh! or if the script wants user-interaction ^^