I have a little bit more info about the AFK fish farm problem. I'm using Minecraft jar 1.8.9 with Forge version 11.15.1.1722. The problem is with the droppers and Forge. In straight up vanilla 1.8.9 the droppers will drop the fishing rods. With Forge installed and no mods in the mod folder at all the droppers do not drop the fishing rods. I tested this out several times and that's how it turned out. Forge does something to either the fishing rods or the droppers making it so they won't drop out. I even did a simple small test. Dropper with a button and some fishing rods inside of it. In vanilla each button push will drop a rod but with Forge nothing happens. I tried the droppers facing all directions and even tried placing the button in different places. Nothing. So Droppers and/ or fishing rods seem to be nerfed with Forge. As for the the issue with iron doors mentioned, I don't have that issue with the iron trapdoor. It is still there for standard iron doors in my version of Forge. Posting a log won't help since there is no error happening that a log would help with. It's something in the code somewhere.
EDIT: I decided to do some further testing. I grabbed the latest version of Forge. Version 11.15.1.1764 and the bug is gone in it. Droppers now drop fishing rods properly.