Cloner staging site does not match behavior of production

When I used Cloner to clone one of our sites in our Multi-site network, I saw this in the log:

Settings Copied
Widgets Copied
Posts Copied
Pages Copied
An error has occured
Terms Copied
Main Menu Menu Copied
Sidebar Menu Copied
Users Copied
Comments Copied

I did not see any information on "An error has occured" referred to. However, I know our staging site does not match the behavior of our production site. The main reason we wanted this plugin was so I could have confidence from testing on the staging site that moving something to production would behave the same way. Now I do not.

For instance, in production we are troubleshooting an issue with some plugins having a conflict with eachother. On our staging site, with all the plugins activated, there is no conflict shown. It is only occuring on our production site with the exact same plugins activated.

I feel like perhaps something important was not cloned over causing this difference. Can someone look into this for me? Or is there a log where I can find out what "an error has occured" refers to?