I have bumped into this problem while was working with huge amounts of layers. I had one big shape-layer, then created a ton of smaller shapes as clipping masks. It went well until autosellect stopped working on most of those clipping mask layers so i couldn't just click on one shape to change it's color, for example. It selected the lowest layer, that main layer with big shape. I tried to turn off autoselection and used ctrl+click but still, clicking on upper layer made the lowest layer selected. After the long fighting with this, I figured out - that happened because some of those clipping layers were hidden. All layers which are upper the hidden layer in clipping mask tree - won't be selected other way than manually in layers window. That's a big problem, it's annoying and doesn't let to work fast. Does anyone know how to fix it at all?
For now, I just have to delete my hidden layers and hope that I will not regret of losing them.
All those layers Shape117, Shape119, Shape122 and upper - can't be auto selected or be selected with move tool+ctrl+click, untill you unhide layer "Shape 116" or delete it. It always selects layer "Shape 114"
As a work-around you could
• set the Layer’s Opacity to 0% or
• apply a Hide All-Layer Mask to it
instead of hiding it,