My point was that you cannot jump to the conclusion that what may very likely be a bug in the application is the fault of CloudKit.
Since you started your post with "I want to add CloudKit to my app...", my recommendation would be to do exactly that. Add it to your app, use it, and draw your conclusions based on how it works for your app, with your data.
It's dangerous to base a conclusion of whether or not to use a particular technology on a behavior in an app that you have no way of knowing what the implementation actually looks like, nor where a particular bug might lie. The issue of lists rearranging in Reminders may very well have absolutely nothing to do with CloudKit, you simply cannot know that for certain.
I'd hate to see you discard a technology that might save you a ton of work and enable some great features in your app based on an impression that might be unfounded.