After playing Samus Returns, Ridley stealing the Baby Metroid from Ceres as soon as Samus dropped it off makes sense. After running away and discarding the last of his cyborg parts, Ridley made a beeline after Samus' route and stole it right away.
The common conception is that the Baby Metroid only held back from killing Samus once it hears her low energy warning, which was its way of realizing who she really was. Except in the previous game, the baby was retrieved after all combat in the game was over. How did it recognize the sound? By Ridley beating the hell out of Samus in his ambush at the beginning of the game, as it's one of the triggers to make his escape; hearing and seeing its mother figure in mortal danger associated the sound with the trauma, which helps knock it out of its hungered state to a concerned one. Incidentally, this sound inevitably plays minutes later when Mother Brain has Samus on the ropes, serving as the means for the baby to intervene after associating the sound with mama in danger.
Mother Brain killing the Baby Metroid seems pretty counterproductive, considering her plans revolved around the Metroids and she just destroyed the last one. However, it goes to show just how dedicated Mother Brain was to killing Samus. The Space Pirates could always find alternatives to Metroids, but getting rid of Samus forever was a prize too good to pass up.
We see in later games that the Galactic Federation was able to retrieve Metroid DNA from this incident too, so the Space Pirates would've presumably been able to do so with ease. Killing the last Metroid was merely a momentary setback.
The geology of the Bubble Mountain room in Upper Norfair makes sense if you look at it as a chamber where volcanic glass collected and trapped gas bubbles as it hardened. The black and reddish-brown volcanic ash that composes much of the rocks is also fairly sensible, as are the reddish-brown cinder blocks that comprise much of the Chozo temple ruins in Lower Norfair.
Crocomire doesn't attack you if you don't attack him and/or approach too closely. Even if you hurt him once, he takes a few swipes at you, but doesn't charge. Crocomire could very well be a peaceful creature and just wants you to leave. Unfortunately, it's not possible to do so until you defeat him, which is just a further point of cruelty on Mother Brain's part.
Even more so, Mother Brain may have left Crocomire inside one of the only rooms in Upper Norfair where the lava from Lower Norfair is visible. And even more horror: Crocomire could have survived the Ring Out if the lava was from Upper Norfair and not the hotter kind from Lower Norfair.
Wow, Mother Brain's time bomb destroyed Zebes! There go all the evil Space Pirates! Oh, and all the native wildlife. Any fascinating biological specimens, any leftover Chozo artifacts, those docile turtle creatures in Maridia, anyone visiting on the other side of the planet - all gone. Such an explosion could also interfere with the orbital courses of other planets and satellites. Well... at least Samus can save a handful of Etecoons and Dachoras if the player so chooses, but it really is a bittersweet ending when you take all these factors into consideration.
Additionally, Samus grew up on Zebes when it was still a Chozo retreat. Its destruction means she loses one of the worlds she considers her childhood home.
By sequence breaking one can explore the rest of Zebes during the countdown and find its inhabitants totally unaware of the impending explosion. More likely it's merely a lapse in Developers' Foresight, but a darkly amusing detail nonetheless.