Significant manual effort is required to include other entities such as suppliers, partners and customers into the overall quality process. What happens when you have non-documented communications such as emails, calls and meetings going on? You only end up with part of the information that may be required to make decisions as you go through. Problem solving also takes longer than it should because it takes too much time to try to find the information by talking to the right people rather than completing the tasks.
With numerous systems, there is an increased likelihood of audit findings. When you make things more difficult for the auditor, they tend to look deeper, have a detailed focus and an increased finding of errors.