Theory:
https://www.mediawiki.org/wiki/Extension:Graph/Demo#Embedded_directly_with_.3Cgraph.3E contains a blue bar <graph> that should be editable in VisualEditor.
Data:
Opening that in VisualEditor, and selecting the graph, produces green stripes of un-editable alienated content:
This is reproducible in Safari 9.0 and Firefox 41 on Mac OS 10.10.5
Noticed that as well but can't seem to reproduce the bug. Even copypasting the same graph in another page on mediawiki.org doesn't get me the same behaviour...
https://www.mediawiki.org/wiki/User:Ferdbold/Sandbox
What seems to happen though is that this particular page treats the <graph> tag as being inline before trying to match it with a mwGraph node. The mwGraph being a block node, it doesn't match anything as the graph is now wrapped inside a paragraph node, so it produces an alienInline instead. Vega still rendering the graph correctly under the stripes, even if it's not a mwGraph, may be a fluke given that there are other graphs in this page, so vega.js is still loaded into this page and searching for JSON specs to render.
Copypasting the same exact area (including all surrounding wikitext) on my sandbox doesn't produce the same result. There, the <graph> successfully gets processed as a mwGraph block, without being wrapped in a paragraph tag. This makes me think it isn't a problem with the Graph extension. Maybe Parsoid?
I checked it again today and that graph works now. Maybe it indeed was an issue in Parsoid and *something* solved this issue?