The Setup wizard is either failing to do a topological sort of plugins, or failing to include optional dependencies in the set of edges.
The plugin manager is not retroactively inserting the class loader for credentials as a parent of that for cloudbees-folder: after everything has been installed we see Failed to instantiate optional component com.cloudbees.hudson.plugins.folder.properties.FolderCredentialsProvider$FolderCredentialsProperty$DescriptorImpl; skipping
Some JavaScript is not accounting for an edge condition gracefully:
Uncaught TypeError: Cannot read property 'firstChild' of undefined
at registerValidator (hudson-behavior.js:424)
at Array.forEach (<anonymous>)
at behavior.js:111
at Array.forEach (<anonymous>)
at behavior.js:107
at Array.forEach (<anonymous>)
at Object.applySubtree (behavior.js:93)
at Object.apply (behavior.js:76)
at behavior.js:71
at window.onload (behavior.js:125)
Probably something else, depending on diagnosis of #3.
Would be interesting to know whether the normal plugin manager/update center do this differently. I've only observed it with the setup wizard but that doesn't mean it wouldn't occur elsewhere.