java fern is very easy to keep and so what you are might be seeing is just bruising from transportation. You could remove the damaged leaves if there arn't too many of them. It will bounce back fairly quickly. It could also be down to lack of food at the lfs and so it will take time to take up the ferts you are using and start producing new green leaves.
If you look at the underside of the fern leaves you'll possibly see brown fur type stuff. This is normal. Java fern reproduces by sending a new leaf, with it's roots, from the tip of an existing leaf. You can allow the new leaf to grow a little and carefully break it off and use this to start a new plant, or you can just leave it be - the roots will attach themselves to your wood and just keep the plant expanding.
Hopefully that makes sense
