Nah, that isn't really a contradiction. He never said they didn't know about the possible existence of extraterrestrials--just that that is when it came to the public's attention. He may have implied it, but to the extent he did, that was clearly propaganda used to try to get the Avengers to calm down and play ball. And that would be consistent with one of the major themes in Avengers (and beyond) as well. If you think it is a contradiction, then fine, but this film is far from the first time that line has been contradicted. Agents of SHIELD and some of the films that followed Avengers have pretty clearly indicated that there were plenty on earth that had been previously aware of extraterrestrials prior to the events of Thor.
In other news, I am WAY past being done with Hollywood/media seemingly obsessing over whether this movie FINALLY makes the important leap of providing us with a lead female superhero, or that movie FINALLY makes the important leap of providing us with a lead Black superhero, or...etc. How about we just enjoy well-written movies about well-written heroes?