Blue Gender

The Mining Station orbits the resource colony on the moon. It's first seen and mentioned in "Versus" after Miyagi and ARK have taken over all the stations except for the Medical.
It's then seen again at the end of "Compass".

Even though Second Earth's Military station was destroyed, what happened to the other 2 stations; The Training Station and the Mining Station?

Why does Amick bother to let Doug out of his cell to help her escape Second Earth when she manages to escape all by herself.

After Director Miyagi Watching Yuji Kaido's data, a messages flashes with spelling errors, instead of Measurement Impossiblity it reads MEESUEEMENT INPOSSIBILITY.

Tony Frost flips a Kenyan gold coin to decide who will complete the diversion mission. The real coin is actually a 10 shilling coin made of silver and features on the front, the second President of Kenya Daniel Arap Moi and on the back the coat of arm of Kenya.

Maybe he put them back on because it was too cold.

Elena said something along the lines of "This is my favorite spot" on the cliff. How is that her favorite if they are always moving around? Just a thought...
The nomadic people in the episode (Gypsies?) could in fact periodically cross the same places, in the manner migratory birds migrate during the season.

Yuji and Elena obviously slept together but for some odd reason, Yuji is still fully clothed when he gets out of covers yet Elena is nude. What's up with that?

If the soldiers are going to burn the food, why not just take it?

Was that Takashi's wrecked bike Yuji finds at the start?

Keith's death is edited out in the edited version. In the uncut version his dead body can be seen in the Armor Shrike.

Keith disappears in this episode. It is unclear whether he is killed or not.

If the Sleepers can only be awakened on Second Earth, how was Yugi revived?