This is not a bug, it is the garrison script. It was implemented in just about all mods and even in later full versions of the Total War games to prevent the player from 'blitzing' the AI. The computer is very bad when defending its settlements is concerned and will leave most of them lightly or even undefended. In order to make the game more enjoyable the garrison script was added. It can be disabled, however.
Read the very bottom of this post and download the campaign_script.txt file and install it.
KGCM Patch 4.2 + KGCM Patch 4.3 Download Thread