That's odd - I don't see it in the iTunes App Store either. It is still posted in the Google Play store for Android Devices.
However, the App Store auto-updated mine (on iPhone) to Version 3.0.09431 just yesterday (June 19 2014).
Just went to add the app to a coworker's new iPhone and also found it missing. I sent an email to Cisco's app support team (email@example.com) and promptly got this reply:
Yesterday we posted an update to correct a couple of issues affecting iOS users. This update checked out correctly in both QA testing and on our Apple Developer site and passed through the necessary App Store approvals. Once AnyConnect physically shows up in the store, it is our practice to immediately test both upgrades and new installs across many devices and iOS versions to ensure everything continues to work flawlessly. Upon immediate testing we noticed that our application was not functioning properly and apparently a portion of our application code disappeared between the Apple Developer site and App Store. At this point the root cause is not yet known (we do not yet know if there is something on our side that needs to be corrected or on Apple's side - we did experience an issue like this once before in 6/2014 and have asked Apple to investigate if this is the same problem or something different). We have had a case open with Apple since yesterday and are awaiting further information from them on their root cause determination. Once the root cause is determined, it is likely that a new version will need to be submitted to them, whether the same exact code with a new version number or after fixing something on our side first if it is determined that an error on our side resulted in this. Unfortunately since the version currently in the app store is truncated/corrupt, the only recourse we had to limit the number of affected end users was to turn off access to AnyConnect. There is no option available to us to revert back to the prior version posted. Since the root cause and solution is not yet known, there is not yet a time estimate for when we will be able to make downloads available again for new installs and to fix users who downloaded in the short period of time when the update was accessible. We apologize for this inconvenience, we are doing everything possible to work with Apple on a root cause and resolution.
So here's my response from TAC:
From the problem description on the case I understood that you are having issues locating Any connect on apple store
We have received some similar cases today, however unfortunately we have no official notification from apple on what happened.
Their website is out of my scope and so the content on it, I will advise you to get in contact with apple support to receive a better answer to your query.
I opened a support case with Apple, They can't tell why Cisco has pulled it or revoked it. I can tell you that Cisco must have there own Apple Developer account in order to publish apps in the App store someone should be able to log in and check on this issue and request status. And the Apple support can't give Cisco Account info. Be nice if they say something.
Looks like Cisco had pull their old version off the store
"An issue outside of our control caused the 6/19/14 update to not function properly. Now that this has been resolved, the same software had to be resubmitted with a new version number. We are very sorry for the inconvenience caused by this issue"
New version is listed in the Appstore, but hasnt fully propagete to the search index yet. Here is the direct link for the new version: https://itunes.apple.com/us/app/cisco-anyconnect/id392790924?mt=8