I've gone into my secret challengers tab but they all seem to be the regular ones/I'm missing quite a few I normally have. Also, when I was battling Canaak it said I'd defeated it one time when I've definitely done so before?

Do you have something in particular that you think are missing? For example, there are some challengers that are in Battle quests that are not in your tab

How long ago did you last battle Cannak, because there have been resets (clearing of battle history) within the last few years, or if it was during a battle quest, battle quest wins don't count towards your statistics.

of course now it seems to be working fine haha. For example I had Ying as a new challenger there but she had disappeared when I was looking at that page and a few of the "normall" challengers were showing up on the secret one too in place of actual secret challengers? In any case it seems to be fixed now.

As for Canaak I think it was probably a year or so ago I battled them last, so entirely possible I've just missed a reset but I'm certain I had since the event when they were released.

There was an alignment issue a bit earlier on which was fixed. The alignment issues made certain rows of challengers appear on the wrong side, so you aren't crazy :P But that issue has been fixed :)