This is what is wrong with this game. Every single player i thinks is an expert and mocks the new ones.

Those missiles were probably defused by someone who attacked you ( spy op - defuse missile). The other nuke was made ( while you play your turns there is a small chance you will produce a missile / you can improve that chance by getting warfare tech ).

Best to do for you is to join an well established alliance, just follow the alliance advertising ( or spam )that will follow my post.