The hole with the yellow gems appears to be designed so you have to keep trying repeatedly until you manage to get the gems. While this probably has no affect whatsoever, the exact way I got it to work was: 1) kept trying until the first gem appeared in inventory, 2) moved that gem slightly away from where it appeared in my inventory, 3) repeated the process until the second gem showed up. I'd wager both gems will always eventually show up with enough fishing into the hole over and over. Why in the world they did it that way I have no clue though. Silly and misleading at best, stupid and pointless at worst. IMO, it should have just been a matter of click on hole, inventory box opens, snatch both gems out.
As for the walking through walls, that's actually supposed to happen in certain places. There are a number of false walls scattered throughout ACT 4 that you absolutely must go through to get to certain places. I recommend dropping a map note on any wall you can walk through for easy reference if/when you need to find it again.
While there are certainly a lot of real bugs plaguing this game, the gem-hole and false walls don't appear to be among them. Misleading and hard to tell apart from bugs, but not actual game errors. It would certainly have helped if they made them clearer however, such as a standard inventory box for the gem-hole and a floating message of text such as "You just found an illusionary wall!" the first time you step through each false wall that's supposed to be there.
