I recently emailed a direct report with no response; I'm way late here but maybe it'll be seen:
If you have Poly and then get Mutant Spider / Inner Eye, your Damage stat is not refreshed immediately (same bug Ceremonial Robes had before being fixed). This is also true for Soy Milk + Chocolate Milk.
Several other items also don't refresh their stats immediately. This includes Blood Bag, Mom's Contact, Small Rock, and The Virus.
3 Dollar Bill activating the Proptosis effect results in half the range you would normally have with Proptosis alone.
Item pedestals should never block doorways - they still can with Beggars and Sin fights.
The stat screen is deceptive and doesn't really convey the information it intends to. In short, the full range of possible values isn't well reflected on the stat screen (e.g., maximum Speed only shows 4 out of 7 bars). I do a detailed analysis here: http://www.reddit.com/r/bindingofisaac/comments/2pxg64/how_exactly_the_stat_screen_works_and_how_it/ , along with proposed numbers that better convey the information. I'm happy to make up altered tables if you'd like me to tweak them in some way.
And a direct bug with the stat screen - Shot Speed affects Azazel's Range on the stat screen but doesn't actually increase the range of his Mini-Brimstone. Ideally, for all characters the Range stat should use the same formula combining Range, Shot Speed, and Shot Height that actually determines Range in-game rather than the approximation it currently uses.
There's a room in the Depths (ID #316) with a Begotten chained directly above the bottom wall door. The layout of this room and position of the enemy suggests there should not be a door possible at the bottom and this room is meant to only be entered from the top.
The Bloat's Brimstone hitbox does not match the visual. Here's an image of it hitting far below the visual effect: http://steamcommunity.com/sharedfiles/filedetails/?id=360597647
And some other issues that are less directly bugs:
The reset button should be assignable to controllers.
Stompy effects should still crush Red Poop while you're flying.
Hitbox size for the eyes on The Bloat and The Pepper is much larger than the visual would indicate. This is an easy fix in the XML - Some testing indicated dropping the value from 27 to 14 would be appropriate.
Red Poop, likewise, will hit you without it visually appearing to, leading to frustration. This is especially true on the top side.
The Lil' Haunt enemies that spawn with The Haunt boss have very high HP for when you face them. Requiring 8 hits to kill at base damage is excessively punishing - I suggest dropping their HP from 25 to 17. This could be done like the Gurglings, where a separate version of the monster exists for the boss, and the other Lil' Haunts still have 25 health.