This bug has been around for a decent amount of time. When you use the Lens of Truth, layers (1 and 2) are not drawn above tiles with flags on them. For example:
-> Lens of Truth -> 
There are secret flags on those four floor tiles (coincidentally, they change to the same tile when you trigger them for design purposes). Anyway, you can see the red trim, which is on layer 1, wasn't drawn when I used the Lens of Truth. Of course, when I trigger the secrets, it looks fine:
Just to show you, there are indeed flags on those tiles in question (as denoted by the big red and orange square):
This is in my 2.10 quest Link to the Heavens if you need it for whatever reason.