Correct options:
* Woke up in the middle of the night. (This is the most natural and common way to say it.)
* Woke up at midnight. (If you woke up specifically at 12:00 AM)
* Woke up in the middle of the night. (This emphasizes the time period rather than a specific time.)
The issue with the original phrase is that "middle" is an adjective, not a noun. We need to use "the middle of the night" as a noun phrase to correctly modify the preposition "at".