The FindLibMongoC cmake helper, in the non-pkgconfig path, uses an uppercase version of the include directory. This won't work properly on a case-sensitive system.
Presently:
set(LIBMONGOC_INCLUDE_DIRS ${LIBMONGOC_DIR}/include/libMONGOC-1.0 CACHE INTERNAL "")
Should be:
set(LIBMONGOC_INCLUDE_DIRS ${LIBMONGOC_DIR}/include/libmongoc-1.0 CACHE INTERNAL "")