What do you think happened at the end of the story, when Madeline Usher appeared?

I assume you are asking why it is that she reappears after she has already died and been buried.  There are three possibilities that I can see:

First, her brother Roderick might have been wrong when he said she was dead.  He might have been fooled by her having one of her spells where she would appear to be dead.

Second, Roderick could have known she was not dead but put her in the crypt anyway, hoping she would die.

Third, she could be a vampire.

Of these, I like the second one best.  I think Roderick is a pretty evil guy and I don't think it would be beyond him to try to get rid of his sister this way.  Maybe that would account for how guilty and jumpy he seems.