This may effect any block with an inventory or tile data, my users have reported it with enchanting tables, signs, and other blocks. But in my test case I used a furnace and I can verify it occurs with that block.

Basically if your plugin replaces a furnace with, say, a chest, and fills the inventory of the chest, the chest will then be empty and you may (but will not always) get this on the server console:

[Server thread/ERROR]: Block at 10,008,134,9,945 is CHEST but has net.minecraft.server.v1_8_R1.TileEntityFurnace@3224f772. Bukkit will attempt to fix this, but there may be additional damage that we cannot recover.

I am not sure the exact build where this started, however I can confirm it does not happen with:
git-Spigot-"606148f" (MC: 1.8) (Implementing API version 1.8-R0.1-SNAPSHOT)

but it does happen with:
git-Spigot-35348a5-e
e6d0fa (MC: 1.8) (Implementing API version 1.8-R0.1-SNAPSHOT)

The code I am using to replace the block is similar to:
w.getBlockAt(x, y, z).setType(org.bukkit.Material.CHEST);
and then filling it with:
InventoryHolder inventoryHolder = ( InventoryHolder ) w.getBlockAt( l.getX(), l.getY(), l.getZ() ).getState();
inventoryHolder.getInventory().setContents( invData.getInvetory() );

Where x,y,z refers to a block that is a furnace.