If you have select report only not block than you will get alert like "would be block". If McAfee AP is blocking anything than it will be capture in logs with right AP detected rule.
More than likely, what you are seeing is an artifact of the application's behavior.
i.e. That it is performing multiple operations, one of which is triggering the AP rule that's in warn mode - but we will allow it. This is not your smoking gun.
"Warn mode" AP rules are benign (but a potential clue to the 3rd party app's behavior).
We do have "silent" enforcement for a certain behavior that applications may exhibit; it was implemented to stop malware.
It occurs when someone tries to "SetSecurity" on a protected file/folder. The attempt will be blocked but not logged.
3rd party application who fail to handle being denied may fail altogether, it depends, but it's not our problem to solve - we can only advise a workaround (disable the feature, or find and disable the rules that are applicable).