I've played FF4 3D recently and here you have to actually DEFEAT an enemy to get it in your bestiary. It seems you only need to see an enemy in Pixel Remaster.

I've only killed the red dolls and the boss but i got all three entries:

• 169 - Calco
  
• 170 - Brina
  
• 171 - Calcobrena

The Tower of Babil map is now separated for two visits. You see the correct amount of chests (16) when you visit it first time:

And then it changes to 8 when you visit it second time:

So you can be sure you get every chest here.


There is a lot of missable entries on every visit (you can find other guides) but the boss of the first visit was really annoying in 3D remake. Since you need to kill an enemy to get it entry you have to complete this bossfight twice (there was an NG+ option for this) with different strategies.

In PR version you just need to defeat the Baranbas and then just wait while Doctor becomes Baranbas-Z. Defeat Baranbas-Z and you'll get all the entries for this bossfight:

• 173 - Doctor
  
• 174 - Baranbas
  
• 175 - Dr. Lugae
  
• 176 - Baranbas-Z

For both Mythril Golem and Lamia Matriarch the wiki says:

Originally posted by finalfantasy.fandom.com:

It can be found on the upper floors of the Tower of Babil after the battle against Rubicante.

Which is inconvenient since you find them after you fall down into the trapdoor in Crystal Room.

I've also found the message on gamespot which says that you may meet both of them in Rubicante's bossfight room but i never got them.

Though you must be extremely unlucky to not meet them here is the exact spot where i found both: