I was like you when I ended the show too! I was like 'what the f***? what is she doing there?'. But then I did a little research and I figured it out. You may know this, but the whole time travel thing was not planned at all, since the season was supposed to end on episode 17, but due to WB orders, the writers were forced to write more 5 episodes. So they rushed things a little bit. That's why it seems confusing. And they forgot about that Elena thing. So, when the DVD of Season 4 came out, they included in it an outtake in which Felicity wrote Elena a note (I never saw it, so I don't know if this is what really happens because I read it on a website, but if it's not, it's something similar.) telling her not to go to Columbia Medical School (where she was in a car accident and died) but to go to Duke Medical School. This question has already been answered here, and months ago I read an answer from someone who said that that final scene was 'real'. It wasn't Elena, Felicity, Ben and Noel who were talking and laughing. It was Tangi (the actress who played Elena), Keri Russel, Scott Speedman... You understand? I totally agree with this! When you see the scene, you can feel the honesty of the 'characters', that they are not acting, they were celebrating those amazing 4 years that they spent together. So that's probably the thing the writers wanted to show.
I hope I could help you because I know how stressful that can be!
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