I've seen it happen to someone else while I was watching a match (one player cast a Benefits of a Spectacle) and I've experienced it personally (casting an Arid Encroachment). In both instances, the spell fired off without a hitch, the card disappeared, flux was taken away, but the enchantment didn't appear in the box (so I couldn't make deserts in the later) nor did it seem to be in play (no glory for spells in the former). This obviously doesn't happen every time.

I also seem to be unable to edit that bug tracking spreadsheet.