i managed to have one of my heroes landlocked in a corner by a "ceasefired" npc faction's city.... apparently you can't just walk through them like your own...

Has happened to me numerous times.  I once trying to link up my cities with caravans but couldn't because Percipenee (or whom ever she is) had packed caravans in my city centers.  There were 3 cities I could not connect.  This also has happened with trying to build on a square, such as gold.  A hero was on it, neutral, and I couldn't access it for several turns because the sod wouldn't move.  Also, if any neutral is in a stack, you can't attack the stack.  You also can't access various buildings in your own town if you have a unit on it.  It's a bit of a royal pain.

I had declared war on a minor to find myself unable to attack the city because during more than 10 turns, a Karavox merchant was parked in the minor capital and I could only select the Talk option for the merchant and not the attack the city. Treaties of any kind with Karavox are usually impossible in my games due to their amazing ability to sky rocket themselves into the realm of uber power.