1. Thinking they own the stuff
It's human nature to make a soulful attachment to our work, especially on a project of as grand a scale and effort as your typical electronic medical records system implementation. An EMR implementation project is often described as a "journey" and can take a decade or more.
The mistake is that IT leaders may forget they are creating a tool to be used by clinicians, not a piece of software design to be admired for its technical beauty. Compromises must be made. Avoiding the dangers of "not getting physician buy-in" is one thing, but truly turning over ownership of the technology to those who use it is a leap of trust that some in healthcare IT are still wrestling with.
2. Putting HIT first
In an industry so woefully behind on automation and information technology, it's a forgivable mistake perhaps that HIT leaders are content at this point to "wire" hospitals and physicians offices for the first-generation benefits of such.
One of the inevitable byproducts of the rush to automate under HITECH meaningful use provisions is that some providers will simply look to "wire up" without taking the time to re-engineer the underlying clinical processes.
The very real fear is that the result will be "really bad healthcare done really fast." The solution is thankfully within reach for hospitals that begin with carefully mapping care processes that need to take place. That process itself has benefits of finding waste and areas for clinical improvement.