Just got the new update, with the store and extra consciousness shards, and it's great. A couple things came up though, which I thought I should mention. I wasn't sure where to post this, and I didn't see anyone having said anything yet, but here's what I've come across.
First, a lot of monsters (clockworks, explosive and lightening espers, etc., but not ameobas and moving fire, along with a few others, I think) drop two consciousness shard drops when they die, instead of one. The first gives actual shards, but the second doesn't. They nearly spawn on top of each other, so it's not something you notice or get bothered by much, as you grab them together, but it does happen.
Second, on missions, the consciousness shard still spawns, but there's none to pick up. So, missions litter the field with empty pickups. Again, not really a problem, but it confused me for a bit, and it's kind of annoying, especially when, in certain places, there are real pickups to be had. It's impossible to tell which is which, and the map is now littered with orange dots, most of which are meaningless.
Third, when an enemy or miniboss is killed in a small corner or right against a wall, there's a very small chance of the shards or upgrade stones spawning in the top left corner of the map, completely unreachable. It's only happened a few times, but I've seen it happen with both upgrade stones and shards. It doesn't matter where the enemy dies in the map, it always goes to the top left corner. The only consistent thing was, the enemy was right against the wall (I was using fireball and energy orb, so there might have been a little knockback into the wall as well) when this happened. The items appear on the map, clearly outside of reach, and in a few hallways where I could get close, you could occasionally see the glimmer of the consciousness shards in the corner (a pixel or two of the right hand side of the animation), so they definitely spawned. It's not common, but it happened a few times.
Lastly, are shards and upgrade stones supposed to fall through boxes and crates, but not water? It always seemed like a bug to me that all the stones just fall straight through boxes, and today, I noticed they'll fall through boxes but float on water, even if the boxes are sitting on top of the water. It's not a huge problem, but it always seemed weird to me.
That's all I found; I hope that helps. Sorry if someone already posted about this/this is the wrong place for this. I had a screenshot or two to add, but they don't want to upload; I'll try to get them up later.
EDIT: Got my images working, I think. Here's a shot of the dual shards; they spawned a bit seperately this time, but they've also come up nearly on top of each other as well.
And this is a shot of the map and log of my pickups after taking out two bosses. You can see the two orange pickups in the top left of the map, beyond any reachable point.