Unless the article left something out, the only possible evidence they had was the wrong username.

It did. The evidence against him were the messages sent to the girl and the unusual username. It's not like it was John_Smith. It was fairly unique.

They couldn't even find evidence that this person used Kik at the time of the crime.

The lack of digital evidence is not proof of innocence. It's not proof of anything either way.

the wrong username

It's very likely the extra underscore was simply glossed over, the way a double space is glossed over. Lawyers aren't generally known for their grasp of computer technology. The lawyer probably saw this a hundred times, thought it was a typo on the subpoena, and didn't put two-and-two together to realize that it was material. After all, the employee at the website could have made the same error but in reverse; assuming that the double underscore was a typo. It's not on the judge, as the judge doesn't go through every piece of evidence checking all the typos; they take the evidence at face value and evaluate its probative value.