There was a MOMC_NO_INVERSE_RELATIONSHIP_WARNINGS setting on Xcode 3 but I cannot find it in Xcode 4.2 and trying to set it as a user defined build setting have no effect.>
Using XCode 4.3:
Find your way to Build Settings
Select project node (top node) in the project Navigator
Select your project under Targets
Select the "Build Settings" tab
Find and set the MOMC_NO_INVERSE_RELATIONSHIP_WARNINGS setting
Scroll all the way down the build settings to near the bottom and find the section named "Data Model Version Compiler (MOMC) Warnings"
The first entry is "MOMC_NO_INVERSE_RELATIONSHIP_WARNINGS" and it defaults to NO
Change it to YES
Build again, and the warnings should vanish.