Are you using the Skill Queue script? Because I have noticed that sometimes that will screw up some skill times. Like if you have skills queued on your home page in one tab and you open a second tab and change skill, the home tab will keep "learning"* until you refresh the page.
* You will not actually be learning the skill, but the bar and timer will still be there and will keep counting down.
I am using the API to manage my skill learning, but I've confirmed that TS sent an email that said "You've finished learning AK!" and that the Skills page (and everything else) (correctly: I already knew I'd be done with AK around 2pm today) says I'm not quite done yet.
I'm slightly pleased to learn that my homebrew script correctly handles changes in learning times better than "Skill Queue"
This has happened to me twice now. My profile feed says I've finished Mining IV but I've still got 11hr 30min to go. No scripts running. Earlier this week it got Better Learning IV wrong.