Google Alerts have been messed up for a while, and it doesn't appear that Google is doing much about it. If they are, they're being very quiet about it, even though others have been vocal about the issues.
Danny Sullivan at Search Engine Land wrote about the issue over a month ago, saying that over the prior several weeks it had become "nearly useless". The main problem is that the alerts aren't returning all the links they should be returning, particularly for those who opted to receive "everything" on the keywords they selected. Sullivan says Google told him at the time that things were improved not long after he wrote the story. Now, they're still not better.
The issue is in the spotlight again today, as TheFinancialBrand.com vented about it in a post that got picked up by tech news link highlighter Techmeme.
Google recently announced it would be shutting down Google Reader, as you probably know. For a short time, Google's RSS Subscription Chrome extension was missing too, though it has since come back. Some were questioning whether or not Google would continue to support the RSS option for Alerts if the company is distancing itself from RSS, though the return of the Chrome extension is a good sign. Another good sign is that Google is actively encouraging others to build news readers.
The lack of action on Google Alerts isn't a great sign though. I remember a similar negligence with Reader, and they ended up shutting that down. Hopefully Google Alerts won't soon be on the "spring cleaning" list too.
We've reached out to Google for comment, and will update if we receive one.