When building a glow squid farm near my base, I found that bred animals prevent the glow squid from spawning, because they use up the cave animal cap. This is a similar issue to MCPE-162501 "Bees block glow squid from spawning".

Steps to reproduce (here in creative mode):

1. In a flat world, allow some animals to spawn naturally in the daytime.
2. Create a 20x20x20 hollow box with a stone floor and at least one side that is glass. Fill the box with water.
3. Move 25 blocks away from the glass side of the box and observe. (Glow squids spawn in farm.)
4. (Optional: examine with NBT editor: naturally spawned animals have surface flag set.)
5. Set time to night to prevent further environmental animal spawns. Breed some (>=4) cows from naturally spawned cows. Separate the baby cows, and then kill the parents and all other animals.
6. Move 25 blocks away from the glass side of the box and observe. (Glow squids spawn do not spawn in farm.)
7. (Optional: exxamine with NBT editor: the bred cows do not have surface flag set.)

Expected result

Glow squid spawn in steps (3) and (6).

Observed result

Glow squid spawn in step (3), but do not spawn in step (6).

 
While it is probably an intended feature that bred animals do not use up the surface cap, IMHO it is rather unexpected that they count against the cave cap.
 
Thanks for listening!