I built and administer large web application which uses the PHPMailer library to send emails via a Google Apps Gmail account. I have received a support request stating that an individual was not receiving a password reclamation email that he had requested.
Looking into this issue, I logged into the Google Apps Gmail account which manages the sending of emails, and I noticed a huge gap in the list of sent emails. The system sends emails through out the day, every day, as users need them. However, yesterday at 1:15 PM, I received two emails which were rejected, and, since then, no emails have been transmitted until today at about 11:45 AM.
I have checked the status page and saw there was a small disruption around 2 - 4 this morning, but not for as long as I've had my problem.
There weren't any error logs generated by PHP regarding this issue, nor any from Google Apps. I also use a legitimate .com domain which does not have any history for spamming.
Any ideas on why this issue surfaced, then doesn't appear to be an issue now? I'd like to prevent something like this in the future, if I can.
You want to prevent this sort of thing in the future? Use a real MTA instead of Google Apps. As you've discovered, it is certainly possible to relay emails through a GApps account, but it's far from ideal, and frankly, it's not what that service was built to do. They give you zero visibility into logs of any sort, which you'd need in order to troubleshoot this issue.
So - you have two options (that I can think of now):
Either of these would give you far greater logging and troubleshooting capabilities if you experience something like this again.
I'd guess you ran afoul of the daily sending limit. Google Apps shouldn't be used for a "large web application"'s e-mailing needs.