Yes, it is wildly dysfunctional.
But, sorry, it is also really likely and the norm for large corporations and having worked in multiple businesses of different sizes, am zero percent surprised by this.
It's so common, it's practically a cliche that as corporations become successful and grow, they become internally dysfunctional and fragmented. In hindsight from the outside, it seems like an obvious problem to avoid, but from the inside, in the thick of it, it is far more the standard than the exception.
Heck, the university IT people I work with are typically re-inventing the wheel about a dozen separate ways across campus because everyone's too busy doing their own job to figure out how to help someone else they never interact with do theirs. You would think upper management would solve this problem, but in large enough organizations, by the time information reaches upper management, it has lost so much detail that they are just focusing on larger strategy and are, of course, unaware of nitty-gritty details. It's simply the nature of large organizations that things get silo'ed, and the communication between silos is rare and at too high of a level to be aware of any nuance or details.
Now it should have been obvious for the D&D team to work with the M:tG team on this, but maybe they did and, again, it was just at a high level of detail of quality vendors, package sizing, InDesign templates, etc. that missed the nuances of making sure to account for humidity when dealing with foil cards.