Bugs

Bugs that can be fixed:

Kobold Lords Pump themselves
Pearl Dragon has wrong pump cost
Spirit of the knight always has first strike
Basalt/Grim monolith have timing issues with the untap
Hybrid doesn't work
Cruel Ultimatum doesn't return a creature
Darksteel Ingot crashes the game if it recieves lethal damage
Incinerate removes a creature from the game
Army of Allah does nothing
Modular lets you target non-creature artifacts
Chromatic Sphere / Star do not check summon sickness when animated
AI is bad at using karoos (Orzhov Basillica, etc)
Many creatures with 'protection from...' are not sleightable.
Rancor does not always return to hand, and has a weird character in ability text
Life gain part of Lightning Helix happens even if the spell fizzles
Tapped Phyrexian Gremlins causes "Wrong parameters" error during AI untap phase
Crypt Rats explosion deals its damage in many 1-point packets instead of all at once
Tolaria is treated like a spell when playing it (can be responded to). It is also incorrectly marked as colorless mana source in addition to blue.
Hellkite Overlord doesn't regenerate
Allay doesn't work with buyback
Reiterate doesn't copy the color of the spell
March of the machines have creates lose abilities

Bugs that can maybe be fixed, but require some new coder skills:

Goldmeadow Stalwart / Wren's Run Vanquisher / Silvergill Adept do not need a reveal to play cheaply
Cloudgoat Ranger is missing 2ndary ability
Gauntlet of Power doubles mana from Dual Lands
Shock lands don't count as basic land types when in play
Progenitus only triggers from play (should trigger from hand, too)
Glimpse the Unthinkable sometimes crashes the game (should be turned off for now)
Creature Bond/Pattern of Rebirth do not interact correctly with leaves play effects (Symbiotic Wurm)
Pattern of rebirth sometimes triggers multiple times
Cards with 'can't be enchanted' instead have shroud

Bugs that cannot be fixed (engine limitations... I think):

Tooth and Nail Entwine doesn't let you play cards from your hand, only your deck
AI can cheat when using comes into play abilities and not choose a target
Comes into play doesn't use the stack
Colored Artifacts show as castable even when they are not
Fetchlands / terramorphic expanse freeze the game for some versions
Cost reductions don't apply to BuyBack and other additional cost spells
Progenitus mana cost looks wrong (but acts right)