I know Butter Brook in Massachusetts had lots of routing issues after discovering an endangered salamander on the property.
From newengland golf.com:
The plan is to begin work this summer on the back nine at Butter Brook, but as of early August the course was still in the process of negotiating with the state of Massachusetts’ Natural Heritage and Endangered Species Program. During initial inspections of the course site, a population of blue spotted salamander was discovered, which delayed construction of the front nine, and now has impeded the backside.
Mungeam, who encountered the same problem at past projects, jokes that the salamanders might be endangered, but the group charged with protecting them, “might not be looking in the right places. They seem to be on most of the proposed golf course sites I see.”
Mungeam has worked with the Kennedy’s to produce a routing that provides the salamander breeding grounds six times the buffer zone required, and the hope is that issues regarding the salamanders will be resolved this summer and work can quickly commence turning Butter Brook into an 18-hole facility—hopefully by spring 2005.