Apple Calendar App keeps reversing alert times.

I also just figured this out for myself after having the same problem. "Second Alert" should mean the second time you are alerted, not the first time. It is counter-intuitive. Apple should just make both alerts independent of each other, so that neither will change the other automatically, and then people can choose for themselves which should be closest to the event and which the furthest from it.

The answer to this question is easy. We have all been assuming that Second Alert was like a snooze button on the alarm. This assumption is causing the problem The "Second" alert is simply an additional alert. The "Alert" entry will always be closest to the appointment. If you set the Second Alert to be closer to the appointment than the first Alert, the app just switches the times. An easy way to remember this is to consider the Second Alert as an "Additional Alert". Why Apple hasn't figured this out I can't say. I spent an hour on the Chat line without getting this description.. Just test it out. You will see it works!

Just got off the Chat with support. Below is the cut-and-paste of the 'fix.'

We will need to reset all settings on the phone before continuing.

What Reset All Settings does: Reloads all default settings: forgets your Wi-Fi networks, removes changes to Alert Styles in Notifications, Turns off Locations Services for third-party apps, sets Sounds, Brightness, and Wallpaper back to original configurations, removes Battery Usage statistics, turns off Siri, turns off Cellular Data, disables Wi-Fi sync, sets Auto-lock back to 1 minute, removes added International keyboards, and turns off all Accessibility options.

Set ALERT for the time closest to the event, then set SECOND ALERT for the time farthest from the event. That has worked for me.

I had this problem too, but it seemed to be that it wasn't reading properly which time I was choosing (as if I might be accidentally pressing the wrong option - big fingers perhaps?). Usually after repeatedly resetting and trying to be very careful which time option I chose, finally it would recognize that I was setting the first alert prior to the second alert. Almost every time I set alerts I would have to repeatedly reset and reset the two alerts until they showed in the right order.

Now I have a new issue. I just updated to iOS9 tonight, and then tried to set an alarm for in the morning. No matter which alert I set for when, both alerts switch to which ever alert I last set. For example, I set the first alert for 2 hrs prior to the time, then set the second alert to 1 hour before, and the first alert will change to 1 hour also. If I change the second alert to 2 hours, the first alert automatically changes to the same time. I have not had this problem before. It apparently will not allow me to set two different alarm times now. I have not yet figured out where I can report this issue.

I have the same problem.

It is now impossible to set two different alert times! Ridiculous! Apple, please sort this out!

I also have this problem.

FWIW, my wife is having this exact problem with IOS 9.2 on her iPad. Her Calendar is also visible on El Capitan 10.11.2, and on an iPhone also IOS 9.2.