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
Sol Kanar has a 'may' ability
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)
Disciple of the Vault is listed as coded... should not be
Many creatures with 'protection from...' are not sleightable.
Ohran Viper text mentions Shadowmage Infiltrator
Rancor does not always return to hand, and has a weird character in ability text
Vodalian Knight doesn't work

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
Merrow Reejery is missing 2ndary ability
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)

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)