Maybe duplicates MC-99728
The bug
In 1.8.9 a thrown Eye of Ender flew to the portal of the stronghold. In the latest versions it flies somewhere to the middle of the stronghold, but not to the portal.
How to reproduce
Open Minecraft 1.8.9
Create a "Superflat" world with this preset
3;stone;3;stronghold
Fly to the nearest stronghold using Eyes of Ender
→ The Eyes of Ender fly to the border of the portal with the spawner next to itOpen Minecraft 1.9 or a later version
Open the same map or create a new
Fly to the nearest stronghold using Eyes of Ender
→ The Eyes of Ender do not fly to the portal
Related issues
is duplicated by
Comments


Confirming this on 1.10. The eyes lead to/near a stronghold but not into the portal. Sometimes there are no stronghold structures at the point where the Eye focuses, and it can be very confusing.
Create a normal world with seed 491058027
Eye of Ender leads to approximately 1864, 32, 840. No stronghold in sight, even if you dig around a bit. There is, however, a very small stronghold near bedrock, having the portal at approximately 1856, 8, 863.

This sounds a lot like MC-70143.

This bug happened first with the 1.9 snapshots. It is probably related but I am not sure if this is really a duplicate.

confirmed to affect 16w39a
since it affects 16w39a now also affects the newly introduced /locate command
The Eye of Ender still finds the stronghold, just not the portal room. The behavior changed in order to support more than 3 strongholds.
I am able to confirm this.