I've identified the issue. There's a bug in BTS where a unit can get stuck joining and leaving a group over and over. It's rare, but it happens most commonly to naval units, and particularly those with hidden nationality. In Moth_in_Bathtub's game I deleted two Tamil Pirates and, sure enough, fixed. Hugfrty's game is crashing for me for some reason, but I imagine it's a similar problem.
I need to figure out whether anything in HR is triggering this bug more often. The Pirate unit is a concern; a hidden nationality unit that can only travel along coasts. Bottlenecks and stacking are almost inevitable.
Unfortunately I cannot fix the bug at its source; that requires the SDK. Someone has written some code that lets the player force units to end their moves with a key press - i.e., if the AI gets stuck in a loop, the player can hit a key combination to break out of it. Not the ideal solution but something I can probably adapt for HR.
I'll need to do more research to see if there are any other methods to fix or bypass the issue, or at the very least, minimise its occurrence.
In the meantime, if your game gets stuck like this I suggest going into the Worldbuilder and deleting some naval units, particularly Pirates or Privateers, and seeing if that allows you to continue.