Getting back to the Windows waiting spinny cursor, with Sigil 1.42 I've managed to reproduce it multiple times using the Restructure Epub to Sigil Norm tool.
Basically, it's an epub 3 ebook where most of the xhtml files start with:
though rather oddly about 13 of the 37 xhtml files do have the xml and doctype lines.
After I click OK on the "Are you sure you want to restructure this epub?" popup, I get a Restructure cancelled: part00xx.xhtml, XML not well formed. After I click OK on that popup, the spinny cursor remains until I close Sigil. Oddly, when I close the epub without saving changes, the part00xx.xhtml is not the same each time I was running this test.
Running Mend and Prettify adds the xml and doctype lines which fixes the issue. I do not have Mend Not Well Formed HTML enabled for Open or Save.
Again an annoyance not a show stopper.