This is a huge problem for a while.
In Hypershade, if you just simple press Ctrl+D when a file node is selected, Maya is duplicated the file node in a very wrong way. Without the isColorManaged flag enabled. (This means you can’t use your nice and useful Color Management System on that particular file node.)
The simple solution:
Go to the Hotkey Editor (really cool) and give shortcuts for Duplicate Shading Network and Duplicate with Connections commands. You can use the same shortcuts in different editors. After that use the shortcuts as usual.
Don’t use the Duplicate Without Network command (that’s the wrong one).
You may have to delete some nodes before or after the duplication.