When I try to delete or copy an application, this prompt comes up.
Have you tried refreshing the page?
yes, multiple times.
I’ve been having similar problems copying apps and creating new ones since about 8:30pm EST. I think you should chill for a minute (or eleventy) and let them take care of it. It’s not expected behavior and I assume the Bubble team will see your bug report and take care of it shortly 
Hang in there.
My submitted bug report has been reviewed and they say that they are working on a fix.
Mine is fixed now.