When using configurable products based on two or more attributes that make up the simple products, the layered navigation ignores the stock status.
This problem allready existed in M1 and remains in M2.
Sample:
Configurable products has 4 simple products (no backorders allowed, do not display out of stock items):
Shirt-Black-S Qty 2
Shirt-Black-M Qty 2
Shirt-Red-S Qty 2
Shirt-Red-M Qty 0 (sold out)
When a users filters layered navigation on color Black and Size M they will still get the configurable product even though the Red M is sold out.
Would be so nice if the layered navigation index would handle this correctly.