These aren't really bugs, and don't seem to fit anywhere (and are painfully minor), but I thought I'd mention them regardless. If this is intentional, well... never mind, then.
The following items aren't... ah... transparent. In other words, they have a black box around them, unlike most other items. I'm sure there's more, but this is what I have handy:
cosmic crystal
fake swipe card
harbor pearl
infernal claw
purple pill
smuggler's box
The Bard's Play
white pill
Zion's helm
The churches are empty / The priest has gone home / And we are left standing / Together alone
--October Project: "Dark Time"
None of the others are actually transparent, either. They're just white backgrounds. This is usually on white, but in a lot of cases (like in messages), you'll see the white show up against a different background.
A lot of times the images have dark backgrounds because either:
a) the featured item is mostly light or wouldn't look right against a white background
b) it looked cooler if it seemed to be "glowing" (crystals, for instance)
c) it's for variety
d) I was lazy and didn't want to do a lot of photoshop work just to change the background color
The first three are fairly forgivable, the fourth is debatable I guess. Still, over time I'm sure I'll do more that way. So it's mostly intentional, and I'm okay with the way it is. There's a couple, like some of the gloves, where some shading gets cut off sharply, and those I think look a little funny and might get fixed, but the solid blacks are okay.
I wasn't sure, which is why I mentioned it. I guess it was the Zion's Helm that threw me the most, as it seemed pretty stark, especially against the white background.
However, the Mochi ball background, at the effect on the demon bat are pretty sweet.
The churches are empty / The priest has gone home / And we are left standing / Together alone
--October Project: "Dark Time"