Messages appeared in 5.3.2p1 version.

Building asset bundles with variants produces error messages in Editor console:

Error message 1: "Use IsAssetAvailable before calling AssetFromGUID"
Error message 2: "Variant folder path cannot be empty if we're building a variant AssetBundle."

Bundles seem to be created correctly, however.

Also, errors don't show if you put the asset inside a parent folder with bundle and variant name (see attached repro project).

Repro steps:
a. Open "asset build warnings.zip" project on Unity 5.3.2p1 or newer.
b. Build bundles (Menu Assets -> Build AssetBundles).
c. Observe errors in console.

Workaround:
To stop seeing errors, move "Material A" inside "Materials" folder and delete/build bundles again.