When you create a new note, two rename boxes appear. One is from your templater script, the other is from Obsidian itself.
How to Solve
settings -> apperance -> advanced -> show tab title bar and turn it on.
Obsidian will automatically pop out rename box if you have title bar hidden.
(guess that’s a feature)
Thanks @zachatoo for helping me solve this problem! Hope anyone meets similar problem - before or in the future - will no longer see those overlap boxes.