In mission 7, on a ledge to the right after exiting the first building, is a box of doughnuts. Shooting it will make it disappear, and cause a giant doughnut to roll down the hill you're walking up.

In the second mission (Battle for Sulaco), there is a hidden room full of facehugger sacs painted to look just like real Easter eggs.

In Mission 6: For Bella, the player enters a large building and has to run past a room with a sentry gun on the left hand side. One of the lockers inside that room contains 3 small balls, one red, one blue and one textured like the ground you run on in the Chaos Emerald Stage from Sonic the Hedgehog 3 & Knuckles.

The reason the Alien AI in the game is broken is due to a one letter spelling error in the game's .ini file. The line is written as

"ClassRemapping=PecanGame.PecanSeqAct_AttachXenoToTether -> PecanGame.PecanSeqAct_AttachPawnToTeather"

when it should read;

"ClassRemapping=PecanGame.PecanSeqAct_AttachXenoToTether -> PecanGame.PecanSeqAct_AttachPawnToTether"

Removing the letter A from this line fixes many of the issues with the game's AI.