It seems that during linking process -Wl,-soname,libmongoc.so.0.4 and -soname,libbson.so.0.4 flags are passed both for libmongoc.so and libbson.so. So at the end of the process both libmongoc.so and libbson.so have the same soname(libbson.so.0.4, the last passed) resulting in linking error when used.

Thanks!