You are correct: macOS does not currently offer a way to disable AutoFill or the "Fill Code" popup for individual applications.
The behavior you are seeing is due to a system-wide feature where macOS automatically scans your incoming Apple Mail and Messages for security or verification codes.
Automatically fill verification codes on Mac - Apple Support
When it detects one, it pushes a global "Fill Code" overlay to whatever text field or window currently has your cursor focus—even if it's a completely unrelated application like Maple. Many users have reported this popping up disruptively in code editors, terminal windows, and spreadsheets.
Since Apple hasn't provided a per-app exclusion list, you have two main options to handle this:
Quick Dismissal (Workaround)
When the little box pops up next to your cursor in Maple, press the Escape (Esc) key on your keyboard. This will instantly dismiss the temporary popup overlay without inserting anything into your active sheet.
Turn off Code AutoFill Globally
If the popup is too disruptive to your workflow in Maple and you are willing to lose the auto-suggest feature in other apps, you can disable it entirely across the system:
- Open the Apple menu in the top left corner and select System Settings.
- Click on General in the left sidebar, then click on AutoFill & Passwords on the right side.
- Locate the toggle that says "AutoFill passwords and passkeys" (which governs automatically suggesting passwords, passkeys, and verification codes) and turn it off

Only Apple can change the behavior. To have Apple consider your feedback, submit it here:
Feedback - macOS - Apple