I am seeing lot of these "incomplete startup packet" messages in postgresql.log in 9.6 version, what does it mean? some thing wrong with server?
It means that some piece of software is trying, incorrectly, to connect to PostgreSQL. The server is probably just fine but you should probably hunt down the other side of the connections and see what is wrong there - or block them if the other end isn't something you want trying to connect to your database.