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Some are burned on previous implimentations that just don't do what they are supposed to do. Your #3 is that about project management software. Going more generally, the company may have put out a new process that was to solve a problem, but made it worse.

Sometimes the new solution has helped management see the business better, but made people at bottom take more steps (introducing more ways things can go wrong). I remember one place I worked where the managers used mice and the admin workers used keyboards for entry. The admin workers felt that they'd never be able to work as quickly and efficiently because they had to do several fancy mouse movements instead of a few key presses.