I've seen that, too, but IIRC it goes away with a good soaking.
What are you using to clean them? Maybe you need to change up every now and then.
With my Better Bottles, I can sometimes see wipe marks on the inside (I clean them with a rag, not a brush) when they are damp. When dry, that goes away. Kind of like when a window steams up and you can see streaks from the Windex.