That wasn't quite it - it was a confluence of events dealing with having this character since just after the beta. A lot of changes have been made to how spells are handled via magic items and so on and so forth. I had a few spells in my spell list that were due to my having a magic item early on (which didn't add to your character in those days, you had to enter the spells in) which I had forgotten to clear out once the Magic Item-spell actions syncing was implemented.
Add to this the fact that apparently since the last time I leveled the character up and now, they changed the Bard's Spell Management to not show Magical Secret spells anymore - not entirely a good move, as this makes it more difficult for a Bard to unlearn and retrain his magical secrets spell for a Bard if he desires at later levels (I believe you now have to so by actually going into the Manage Levels section and changing out the spells in the relevant levels, which still lists all the non-Bard spells without any tags as to spell source, so you'll have to have another tab open).
Tl;dr: not broken, just changed from what I had been used to for the past year and a half.