There are no secret passages on the second level of Iona's dungeon. It sounds like a clipping issue, though I don't recall anyone mentioning gaps large enough to walk back and forth through freely.

Iona's dungeon maps: level 1, starting cell level and levels 2-4

Sometimes there can be gaps in the north west corner when 2 wall meet, large enough to talk to someone on the other side (if you stand in the right place), and maybe toss a teleporter stone through. There are also rare pathfinding glitches that can have your character jump through a wall.