Hello,
I’ve tried to add categories to the menu on default theme and the issue is present there too. It can be caused for the reason you’ve increased the menu items limit. That’s why new items can’t be saved. Here are some explanations:
http://www.wpbeginner.com/wp-tutorials/how-to-fix-the-custom-menu-items-limit-in-wordpress/
https://core.trac.wordpress.org/ticket/14134
Regards,
Eva Kemp.