I've got first hand experience in this as we are working on it right now.

This problem is largely due to the closed and archaic nature of the GDS systems that are the source of truth. These systems have been running for 40+ years and no one wants to touch them to make substantive changes. As a result, modernisation is attempted via layers on top of layers that just add complexity confusion.

There is a difficult routing and fare calculation problem here, coupled with a distributed consensus problem. While better solutions to this exist or may exist, the biggest hurdles are the organisational ones.