[tomek]

When using a sep funnel doing extraction, washing or whatnot, do you collect that fluff that gathers at the interface of two layers?

[TheUnassuming]

I don't usually make any special attempt to keep or dispose of it.  Since you will be drying over sulfate/filtering your organics before concentrating, it shouldn't affect your outcome either way unless the fluff is your product.  In that case you need to modify your workup conditions anyhow.