Hmmm, I have forgotten about that. I have this problem on Version: 0.41.1 (build 15919) using Mercury 126.96.36.199. I have linked a video at the base (for a time) to show the process of recreation but basically the steps are;
Enter the menu.
Create a new menu item, with tag link as the type and tag of the same name as the menu item and then drag it into a sub-menu position.
Click preview your pages and the menu item appears last in order even though it isn’t in Publii. If you close and then reopen Publii and then enter the menu again, it appears both in the place you dragged it to and last in the list. If you delete either of the duplicates it deletes the other.
It is not totally consistant, I have added other menu items since first trying my menu item ‘Recloses’ but it does seem to be consistent with that menu item. Anyway, watch the video.