While I would not necessarily consider this a "downside" to integration, the largest obstacle that my organization faced was resistance.
Resistance to change.
Resistance to a perceived loss of responsibility and authority...thus "power".
Resistance to knocking down the silos or walls between departments.
Our organization had many departments and people that were "old school". Their areas were their territory. There was a lot of resistance to sharing ideas, communicating, merging systems/tools/methodologies.
We applied the formula C + V + D > R, where if C, V and D are done properly, R (Resistance) can be overcome.
C = Current state - convince the people that the current state is inadequate, does not meet their needs and must change.
V = Vision - how the future system will be better, make lives easier, and help the organization.
D = Do it - a detailed plan and strong support to help people move from C to V.
Another issue that we discovered, was that while integrating merged much of what we used, it did create a large, all-encompassing system. This allowed those people who wanted to keep their "silo world" intact to create tools / standards / documents...a larger system created some hiding spaces for these people.
To resolve this situation, we adopted an integrated, layered audit process. Several levels of personnel are involved in different types of audits, while maintaining a focus on quality, environment, safety, financial, etc.
We also took those people who were desparate to hang on to their "silo" and moved them into positions that promoted coaching and facilitation instead of old school supervision / management. This gave those individuals more exposure to the system and promoted understanding.