I've been using Xisumavvoid's updated "Lossless cooked chicken farm" on our old rented Craftbukkit server just fine. However, ever since I updated to Spigot our baby chickens seem to be getting sucked back into the dispenser and suffocate then die so they never get big enough to cook. When I switch to a vanilla server or back to Craftbukkit it works fine again.
Looking at the comments on YouTube it appears other Spigot users are experiencing this same issue.

For testing I setup Spigot 1.8.7-R0.1 - snapshot on my Windows 7 SP1 desktop (Intel i7-3770 CPU @ 3.4 GHz 10GB ram) and copied over my world files to test to see if it was a problem with the rented servers files. The farm still has the same issue. it fired an egg into the holding cell. When an egg hatches the lil chicken sits there just fine until the egg dispenser fires another egg at which point it sucks the first little guy back in and kills it.

I then deleted my world files in case something was corrupted and restarted the server with a new world and the dispenser is still buggy. Sometimes it shoots the baby chicken with lava in it's head. Sometimes it sucks it back in. And sometimes it works fine when it fires an egg. But eventually all the babies will get sucked in and killed or burned prematurely. I even had some that somehow fell through the blocks completely and ran around outside the machine!

Again, I verified it is a Spigot issue by running a vanilla 1.8.7 game in both creative and survival modes and the chicken farm runs flawlessly.