Spoiler
1. Why are 2B's (and the other E type units') memories not wiped after every execution? It seems like the mental turmoil they undergo should be predictable, and 2B in particular seems like she would be willing to undergo memory wipe. Androids and machines are both capable of undergoing memory wipe.
9S units effectively have their memories repeatedly wiped because they get executed and then freshly produced with a blank template personality. But they're still useful after having lost their memories. Why wouldn't 2B still be useful after having lost hers?

2. Who in the world is stocking the half-empty supply crates destined for the moon? In short story Orbital Bunker Observation Diary (https://theark.wiki/w/Orbital_Bunker_Observation_Diary), the Commander personally approves a supply shipment to the moon, which is reported to her by an Operator type. This implies that the androids themselves are involved in stocking and shipping these supplies. How would they not notice that there aren't enough supplies in the crates to support a colony of humans?

3. The first time we see a black box reaction in the game, I was a bit disappointed because it was so OP. All of that sword and gun combat seemed meaningless when you can blow up 3 goliaths with 2 black boxes. Have YorHa ever tried launching black box missiles, or bunker busters, to target important machine targets/factories?
(Note: It's explained in game that long-distance lasers orbital strikes are not always feasible because machine units can energy-shielding. However, we haven't seen anything in the game that can resist a black box reaction explosion.)
^ Possible reason - the black-box reaction completely destroys machine cores, which makes it impossible for YoRHa to collect more for the purposes of black box production. Maybe Command probably wants to avoid wasting machine cores that could be used to produce more YoRHa. The flaw with this reasoning is that: there are so many low-level machines wandering around aimlessly on the overworld. You can harvest cores from these weak units, while using black box reaction missiles on harder targets without wasting nearly as many YoRHa. (On a side note: I wonder which YoRHa units actually collect the machine cores from machine corpses, or does it actually work like in game, where you pick up the machine cores yourself and sell them to the resistance. Has YoRHa figured out how to synthesize machine cores yet, or is harvesting them from machines the only way to get them?)
^ Possible reason #2 - one of the big reveals is that this generation of YoRHa is meant to gather as much battle data as possible, before being intentionally destroyed by a logic virus.

4. How do Logic Viruses work?
Is this a generic term that can be used to describe viruses produced by the Machine and YoRHa, or was it uniquely produced by Machines, and then isolated and utilized by YoRHa.
In the short story Memory Cage (https://theark.wiki/w/Memory_Cage), the Commander forces 2B to use a logic virus and a "closed barrier"
to trap 9S inside her mind and destroy his personality with the virus.
But despite having a Logic Virus in her head, she was doing absolutely fine until her fight with 9S.