Okay, the ship that they discovered was indeed a Space Jockey ship. It was actually the same one from Alien. People have moved to the planet and started to habit the planet with colonies. The hamsters? that scene was inside the colony itself. When the guy got infected, he was brought back to the colony where the Xenomorphs grew in numbers and attacked the colony.
I get the feeling you didn't really watched Alien (not as an offensive comment, just something I noticed). It was the same planet in both movies. And as for 300 years? Ripley didn't sleep for that long did she (I remember it was only 57 years)? If you're talking about the time between AVP and Aliens then that's a different story.
"There are five possible operations for any army. If you can fight, fight; if you cannot fight, defend; if you cannot defend, flee; if you cannot flee, surrender; if you cannot surrender, die."