I had a similar problem to yours mate, and sorry for not getting back to you sooner Anabasis. It happened to me when Rhodes declared war on me in the 20th turn in my Macedon campaign. I arranged an army and set out to see what I could do against that, sending a spy (on a different path) as a recon. After noticing that, disregarding the seasons, my army was MUCH slower, i.e. had less movement points, than on land (I figured that somewhat realistic (?) as commanders on land have less experience at the ways of the sea than naval commanders), I began to make my crawl over to their island. My spy, having scouted the area, could not encounter any armed forces except for the garisson. I figured that this was my chance! I managed to get within "one-turn-range" of the settlement and began preparations, including sending in my spy to sabotage. The next turn, however, I could not attack due to unseen reason. I was in range with my fleet and was planning to auto-resolve the siege as I had already sabotaged their garisson twice but it was denied to me wholly.
I had another incident regarding this matter whilst early on in my Macedon campaign, conquering Antheia. However, there I figured it must've been the enlarged reinforcement zone that prevented me to attack, since the zone markers from two armies outside the settlement and the garisson's zone marker tightly overlapped each other, resulting in said enlarged reinforcement zone. It simply confused me, since there was no indication regarding the movement-line that an attack would not be possible.
I would highly appreciate this mate! This mod makes the game increasingly enjoyable. Maybe there is a way to give the AI (and ourselves) an option whether to send the garisson out to reinforce the attacked/attacking army or not. However, given the "freedom" you have to modify this game, I don't think that would be possible in the near future. Nevertheless, I can only repeat myself. Great mod. Can't wait for DEI 0.7 and according implementation/updates for this mod.