Sorry it's taken this long to report this. We didn't know about it because it was invisible until we tried to build in that area. Ops can break/place blocks. Players can only break blocks but not place. Confirmed that it's spawn protection related by reducing spawn protection size which then reduced the area. Players could then successfully break/place blocks. This happened when we first installed spigot 1.9.0 on a fresh survival world. No idea what other plugin could have caused it. I've looked in configs for essentials, multiverse, and worldguard (no regions in world). Even loaded up NBT explorer and explored the rca and nothing in there either. I've been from bedrock to skylimit looking for a spawn point. It seems to have duplicated our survival world spawn point and moved it over somehow. Can't figure out what could have caused this or how to fix.

Multiverse-Core 2.5-b719
Multiverse-Portals 2.5-b742
EssentialsX 2.0.1-b330
Vault 1.5.6-b49
WorldEdit 6.1.1-SNAPSHOT;3459-94ae1be
WorldGuard 6.1.2-SNAPSHOT;1652-c9b8e9f