What does Mikasa mean by "It's happening again" in the 2nd episode? At the beginning of the 2nd episode after Eren and Mikasa are saved, the blond army guy pulls them forward, and Mikasa holds her head, has a flashback, and says "It's happening again".

What does she mean by this?
After I rewatched the episode, I can firmly answer your question but be advised for there are spoilers in my answer. 

When she has that flashback, 


   she remembers how her family was murdered and she was thinking that she remained alone, until Eren saved her and she became part of his family. When Eren's mother dies, Mikasa experiences the same feeling of losing someone dear as she felt when her family was murdered. This is why she says "It's happening again..", because she lost a part of her family again.