Not only does that mean Ali lied to the girls about her travel pans (after all, we already knew that), but it means she had many extra hours in Rosewood when she was supposedly on a bus. We can pretty much assume that she didn't use that extra time to catch up on her beauty sleep, so what was she doing?
Here are our top three theories:
Confronting "A": It seems clear at this point that Ali was trying to track down "A," and Duncan did say that is seemed like she had figured something out on that plane ride back. Maybe she had finally pieced together the clues, and used that extra time to try to confront or otherwise intimidate "A." If this is the case, than it seems like "A" probably did have something to do with her disappearance, too.
Dealing with N.A.T: From the videos the girls found, we know Ian (Ryan Merriman) and Ali were together, but having problems revolving around Ian's N.A.T. activities. Maybe Ali was spending her extra time trying to navigate that whole convoluted relationship.
Confronting one of the Hastings: We're still suspicious of basically every Hastings not named Spencer (Troian Bellisario). Maybe Ali used that extra time to deal with blackmailing Spencer's dad, or to confront Melissa (Torrey DeVitto). And then maybe an angry Hastings got their revenge...