I have my criticism on the game, but some of these seem odd to me:
Zhent:
Why wouldn't the Zhentarim mine the bottom? They already have supplies close to the upstairs area, wouldn't want to damage those. I think this is fine.
Last Light:
Timings working out like that is just something that happens in every narrative. Could as well ask how Frodo in the novel just randomly left right the moment before the Black Riders arrive. If you want a rationale, the timing of the attack makes sense since Marcus was able to observe Isobel on the balcony, so he knows exactly where she is. It would have been awkward attacking the place and look around for her since she is just on the loo.
The Black Riders are actively seeking the Ring are they not? They do not just happen to turn up out of the blue. I agree that timing plays a part in story-telling (even in BG3) but too often in this game it is too contrived.
Zhent.
Because the people laying the mines would be exposed while laying them and would have to scramble back up the roots if attacked (by the minotaurs that are mere metres away?). Anyone with a gram of common-sense would place supplies beyond the blast area of the mines.
Last Light.
Why does Marcus need to attack at all? Thorm is the brains behind the attack. Why does the shield collapse? Isobel is on the balcony but the fight takes place inside an inn full of Harpers. Why is the Shadow Curse there at all? Why has nobody done anything about it?