MDE/Disney guest information systems infrastructure is problem prone. This occurrence was yet another example of it. The heart of the problem, is a system that was over promised and under designed. The fact that it is common for people to call tech support to fix their vacations speaks volumes about what has been implemented.
I can only comment on the ticketing systems but a lot of what you say is true from what I hear. Disney have a lot of software platforms built at different times some with great API's and others using some cobbled together integrations all trying to talk to each other so your tickets, hotel res, fastpasses and dining are all connected but in reality they are not all in the same database. In an ideal world Disney would build a system which can do all these in one and your full record of everything is one place. Until that happens I think they are going to stretch the systems to the limit in order to avoid addressing an expensive issue.