Yeah, I thought it was that bug, I almost never see AI trade routes either, so I agree with you that it doesn’t have anything to do with that.Yes, it's that bug. The AI goes crazy for science, so it doesn't build CHs and other financial sources. The units get crazy expensive compared to their income so they go bankrupt, disband their army to try and recover their finances, but never rebuild, they end up stagnant.
I'm not sure trade routes have much to do with it, to be honest. The AI was given too much focus on science (150 instead of 15, I believe), so it just collapses.