Defeating Mother Brain causes minor issues with LttP inventory

As reported by Iris Isotheis:

Seed 163329366 (v10, normal, random morph) Using snes9x 1.56.2

Found nothing in Aginah's cave.
Save + Quit. Reset when on menu, after making sure it was loaded (triforce pieces animation).
Picked up Varia and a bottle in SM.
Transition back to LTTP. All fine. Checked Sick Kid then farmed for Zora.
Picked up Flute at King Zora.
Picked up Silvers at Zora ledge
Played in SM from Norfair portal, did pretty much the whole game. Picked up every unique item, except Somaria, Tempered/Gold, Half-Magic, Mitts, Powder, Cape, 2 bottles, both boomerangs and Ice/Wave/Spazer/Plasma.
Killed all four bosses. Killed Mother Brain. Checked blue brinstar, farmed for 2 Power Bombs, and checked crateria supers.
Transitionned to LTTP via Crateria portal.
Item box was empty.
Pressed Start to open inventory. Immediatly, when slide started, Bow appeared in Inventory (Silverless).
(I now notice Shovel also appeared, instead of Flute. Cannot tell about Mushroom, didn't have Powder.)

I remember there being some discussion about the MB flag set disturbing other things, but I can't recall if it was this issue specifically. Best guess is that the MB flag set is stomping on some other trivial state values or perhaps using some obsolete cached state? I'll try to recreate it and get a BSNES save state so we can look at it more closely.

tewtal / alttp_sm_combo_randomizer

Defeating Mother Brain causes minor issues with LttP inventory #71