I think something similar might have just happened to me. I created a new project today and copy-pasted around 30 notes into it (with dates going back to 2015). The note with today’s date was stuck at the top, while the rest were sorted from oldest to newest (second newest was at the bottom).
After reading your suggestion I moved today’s note to tomorrow. At that point it sorted correctly (at the very bottom). After that I changed it back to today and it remained in the right place.
Before changing the date I exported the project to an .agenda file. So if it would help you in any way I can try to reproduce by reimporting (or I could just send you the file, there is no sensitive/private data).