I have Moodle 3.3+ (Build: 20170608) and PHP Version 5.6.31 installed on our platform and we are also having this exact issue. We found if you Purge all caches it will allow you to delete the course, however, this is painful if there are many courses being deleted. What theme are you both using? We are using the Adaptable theme.
I have not seen any thing on a permanent fix for this issue.