I ran into this problem and ruined a bit.
I built with Xcode 6.4, and it looks like previously the main data only generated the .mom file in the MyApp.ipa momd directory. This screenshot is taken from a project that saw several versions of Xcode.
Please note that all older versions of the model only have a .mom file. I just created a new version of the model today, and it has both a .mom and a .omo file.

It seems that Xcode 6.4 (and maybe some of the beta 7.x versions) do not know how to load the optimized version of the data model, because I also get
2015-10-16 11:11:42.563 MyAppName[1767:599635] CoreData: Failed to load optimized model at path '/var/mobile/Containers/Bundle/Application/D887D60B-FB28-4059-8167-F573460D98F8/MyAppName.app/MyDataModel.momd/MyDataModel3_0Analytics.omo'
warning when compiling with 6.4. However, when compiling the application with the latest version of the Xcode application (7.0.1), I do not receive this warning. I assume the reason for Mahesh's solution is that re-writing the entire schema creates the .omo file that the application is looking for in the application bundle.
The solution for me was to generate a new version of the data model in the master data, and then build using Xcode 7. It seems that creating a new version of the model creates an optimized model file. In my testing, although even with this file created by Xcode 6.4, an error still throws. It was not until I tried it with Xcode 7.0.1 that the warning disappeared.
This is an assumption, but I think that if you have an existing project and you have not created a new version of the data model and have not created with Xcode 7 that the .omo file is missing, it throws a warning because it cannot find the file. However, if you checked the version of your data model and created with Xcode 6.4, it seems that an earlier version of Xcode does not do something right with the optimized version, and it does not load it, even if it is. These are just my observations.
I checked that I had an optimized model (.omo file) for downloading by doing the following: 1. archive your project 2. change the .ipa extension to .zip 3. Expand your zip file 4. Click on the "payload" folder and right-click (or see. Click) in the application bundle in the folder and select "Show package contents". 5. click on the .momd directory, you will see all available models of managed objects.
If all you have are .mom files and .omo files, then the warning makes sense, the application cannot open a file that does not exist.
In my testing, it seems that the warning was only informative. Because of this, I never came across this. It looks like the kernel data might try to load the optimized model first, and if that doesn't work, go back to the regular .momd model. This is just my guess.
I'm not sure that everything here is completely correct, this is what I have observed so far, trying to debug this. If anyone else can contribute more information, I welcome your input.