The underlining bug has been logged–it seems that when the first word of a paragraph has special character formatting, the carriage return is picking it up and then not letting it go, even when you remove it in Scrivener, so the whole paragraph ends up with the formatting.
As for the ungroup, it sounds like it did exactly what it’s supposed to, so unless I’m misunderstanding, that’s not a bug. Ungroup takes the contents of the selected container and moves them out of the container to become sibling items with the parent container; the parent container remains (empty), so you should be able to just drag the items back in to correct the mistake. To view the subitems along with their containers, try just selecting the folders and their contents in the binder and viewing the multiple selection on the corkboard.