i've experienced the same thing. usually i try to set up or have it set up a milestone/phase approach to an implementation with checklists (markdown style) but it's 50/50 if it marks them automatically upon completion.
I have this in my CLAUDE.md and it works better than 50/50. Still not 100% though:
### Development Process
All work must be done via TODO.md. If the file is empty, then we need to write our next todo list.
When TODO.md is populated:
1. Read the entire TODO.md file first
2. Work through tasks in the exact order listed
3. Reference specific TODO.md sections when reporting progress
4. Mark progress by checking off todos in the file
5. Never abbreviate, summarize, or reinterpret TODO.md tasks
A TODO file is done when every box has been checked off due to completion of the associated task.
