A few bugs affecting Alice as of the time of this post: Vanilla glass (minecraft:glass) will accept items into its stack, but instead of increasing the stack count it destroys the blocks added. This occurs in various machines, player inventories, etc. Vanilla bottle (minecraft:glass_bottle) recipe yields 1 bottle per craft instead of the expected 3. Potion ID conflicts in Witchery are causing wearers of Bound Armor fitted with swimming runes to spawn Nightmares, among other issues. (I believe this fix has already been submitted.)
I have no idea what you mean about the vanilla glass part, lol. As for bottles, I'll fix this soon(tm) The Witchery potion IDs are fixed in the next update.
Regarding vanilla glass, it's a very strange issue. Say you put a stack of sand into a furnace; the full stack will smelt, but the output glass stack will remain at one block. If you try to combine two blocks of glass in an inventory, they will stack together, but the resulting stack will remain a single block. This numberless stack can't be split, and is as far as I can tell indeed a single block of glass.
1 - You can't pick up oil with a bucket. 2 - You can't turn oil into fuel with the refinery, because the oil won't enter it. It's apparently being worked on by LordRedstone, just figured I'd put it here to be marked off on the checklist we're compiling.
I've never seen that problem before, and I've used and made a ton of glass o_o It's fixed in the next update. It was a PneumaticCraft bug and was fixed by the author, so I updated to the latest The "next update" I keep mentioning is basically updating every mod in the pack, so stay tuned.
It's a very recent issue, I only noticed it late last night. Seemed to crop up after sk made the changes he did, but I wouldn't think that would be related.