In an Island Explore mission, I have the option to trade some of my Wood for Marble in the game. It says that my inventory is full but it shouldn't matter because I already have both Marble and Wood.

I noticed a similar provlem with the Scriptorium - it'll be asking to trade one blueprint I don't have for another that I have only one of, and it will block me from confirming the trade if I haven't got an extra space in my inventory. Of course, swapping one blueprint for another shouldn't require any extra space.