We just enabled Lightning today and I noticed two things right away that appear to be "bugs".  #1) Despite the fact that our Sales app is set as default for my profile, Lightning opened in one of my other apps first.  I had to open the menu and go to Sales manually.  #2)  The App Menu is not in the order we have it showing in Setup.  I have Sales as the top app in Setup, but when you click on the square dots, it appears in 8th position.  Has anyone else experienced this?