I can confirm this post Fall patch problem with assigning spies and trade routes.
Was using 22 mods that were previously safe with BNW, and kept experiencing this glitch. However, after dropping all mods and restarting the game, everything was fine.
Also tried to narrow it down by eliminating a few mods at a time, but with 22 mods that became too big a hassle, so I stuck with playing without any mods.
The mods I'd previously been using were:
Barbarians - unlimited experience
City-State Diplomacy Mod for BNW
Colored Religions
Goody Huts - No Maps
Improvement - Farm Replacement
London Eye Wonder
More Luxuries
More Pantheons
National Park
Oktoberfest for BNW
Piety Buff
Pikeman to Musketman
Policy - Free Archer
RED Modpack
Resource - Mint Include Copper
Smithsonian Institution
The Olympic Games
Trafalgar Square Wonder
Units - Cheap Workboat
Wonders - Disney Pack BNW
Wonders - Museo del Prado BNW
Wonders - UN Headquarters