First is that companies don't have their processes straightened out. In every reasonably large project I've worked on, the greatest bottleneck has been trying to write the business rules. For instance: The company directory that couldn't go online because the phone numbers, department assignments, secretarial assignments, office locations, etc. etc. etc. were all maintained by different people, in different formats ranging from databases to spreadsheets to WordPerfect files. No one would give up their little piece of control (power) over "their" information.
Computer systems rely on concise, or at least unambiguous, rules. When the existing business practice doesn't fit these criteria, it's not ready for automation.
The second problem, which depends on the first, is that software vendors tell companies that they can replace expensive, experienced personnel with some new product. The reason this works is that no business wants to believe they are guilty of the first problem I mentioned. "Since our processes are well thought out, they can be automated."
Your multi-billion dollar pharmacy company has gone to step three -- replace the experienced people with shaven monkees -- without going through steps one and two -- standardize the process and automate it.