The incident happened after the swan station was built. The Proof is in the orientation video.
"However, not long after the experiments began, there was an incident, and since that time the following protocol has been oberved"
There's also proof on the blast door map. http://lostpedia.wikia.com/wiki/File:Cleanwall-707484.jpg There's a note that says: "I am Here". It points to the Swan station. Directly below that note, it says "Multiple escape conduits blocked after incident"