Issue:  The last 2 games this has happened to me, last time with the Wind Walkers, this time with the Necros.   I siege the enemy AI town to 0 fortifaction, and there are 0 troops in the town or region.    When attacking the town, expecting to take it over, the enemy magically will have troops to defend, every time, turn after turn after turn.     Usually, there are 2 new militia every turn, sometimes, there is a smaller army with or without a hero.   Every attack I get a victory, but the town does not change ownership.  I have tried to stop the siege before attacking, walking away from the town for a turn, but none of this seems to matter.  I have a couple hundred hours in this game, before the issue just began.

Specs: Q6600 Core Duo Quad Core 2.4Gh 8GB RAM AMd Radeon 6800 driver 15.201.1151.1008-151104a-296217E Win 10 Pro 64b

Version:  1.5.6 S3 64 Bit

Video: https://youtu.be/VRzk_LaFfPM

(recording is laggy on my old toaster with this game, sorry)

Sounds like you are experiencing the same issue I encountered. Here's my post, https://www.games2gether.com/endless-legend/forum/22-gameplay-and-ai-issues/thread/22207-city-will-not-capture-when-reinforcement-participate-on-defending-side.

To get around the issue you hit you'll need a second army to siege the reinforcing city.  This will prevent the militia from re-spawning and allow you to capture the city once there are no units to reinforce the city. Hope that helps you.