Hi,
As per recommended guidelines listed in in-place upgrade we need to perform upgradation on a clone test environment.Steps are to take required backups from AX 2012 RTM, install CU12 on test environment, run setup again to upgrade modeldatabase, upgrade base layers and models(& ISV's if any) and last step is to include custom models(in each layer). I believe conflict is happening between some base objects of two versions. Please check the in-place upgrade process listed below(as suggested by André) to see if any step is missing.
Refer following link - Check for case Upgrade from AX 2012 or AX 2012 Feature Pack.
(Scenario: Perform in-place upgrade to AX 2012 R2 or AX 2012 R3 [AX 2012])