The greatest difficulties are those outside your own discipline. For example being a clinical chemist/clinical pathologist and responsible for a large laboratory I have encountered great problems when the ICT department shifted to WINDOWS 8 based software that stopped particular but very important lab server when that was not used for 8 hours (e.g. in the night).
No solution preventing all future trouble but I managed to get a better information exchange with the ICT guys.
The lack of respect for what we know and do. The laboratory has very strict standards for collection and handling as required by the testing process and accrediting agencies. We have many problems with other departments not wanting to follow those standards and therefor provideing less then optimal specimens, which then, may produce low quality results.