Continuity mistake: Charlie has set up a "security system" on the right side of the bed. When a double slaps Lindsay's hand, she goes over to a chair on the right side of the bed and the security system has vanished completely. It reappears when she returns to bed.
Continuity mistake: Notice how Julie pumps her shotgun twice within a few seconds in the lab without once firing.
Continuity mistake: It is mentioned in dialog that during the last bird attack (the first film), a red rain was visible that seemed to drive the birds mad. However, at no time during the original film is there any red rain visible.