I have just found out that if you delete an alarm in the todolist it doesn't actually do anything. They appear to have been deleted, but if you go back into that item they are back, or if the time comes the alarm still goes off. I know the solution to this would be to change the date to one that has already passed, but it's not supposed to do this, and if many alarms have been set it can be a bit annoying having to change the date on all of them rather than tapping delete a few times.
There doesn't seem to be a problem with the calendar, but this sets the alarms differently.
I have also noticed a similar problem with the clock alarms: they may still go off even if enabled is unchecked. The workaround for this is to unselect all the days.
I know there was a suspend bug associated with the alarm system, but I haven't been able to find any info on this problem.