I know the timeline is screwed up, and it doesn't bother me that much, I just have a personal bone to pick with enemy discontinuities because I run a website about them. Here are some other stupid questions that have plagued me over the years:
Is Birdo a cross-dressing guy or a girl? (Nintendo has settled on girl which is good enough for me).
Are they Podobos or Lava Bubbles?
Why did Koopas suddenly start walking upright?
Why did Cheep-cheeps become Blurps in Super Mario World? Why did they introduce a new enemy called Cheep-Cheep that wears goggles and is green?
Why are Goombas impossible to stomp in Super Mario World? (That game screwed up a lot of enemies)
Why do all the Koopas in Super Mario RPG wear armour? Why are they called Terrapins?
Are they Beezos or Shy Aways? (Super Mario RPG also screwed up a lot of enemies)
Super Mario Sunshine and Super Mario Land really screwed things up too, but that's enough pointless complaining for today.