When mousing over a potential item to craft it will flash/highlight your inventory if you already have such an item. If you click to craft that item, the contents of your inventory could change as items are consumed in the process. However, the highlight does refresh itself when this occurs and it continues to highlight the same space... This leads to it highlighting either an empty space or the incorrect item.
Screen grab, notice my mouse is hovering EM3 but it is highlighting empty space
[0.10.0] Highlighted item in inventory is wrong
Re: [0.10.0] Highlighted item in inventory is wrong
Thanks for the report, this will be fixed in 0.10.1.