Brenda will be taken hostage if enemy recaptures sector 28 after Brenda's gone back to work there (the next day after you liberated it) and you don't recapture it on the same day. This can happen on easier difficulty too, but it's a lot more likely (if not inevitable) to happen on harder difficulty. On harder setting, enemy will attack this sector almost every day as long as they succeed until you have captured all the surrounding sectors (of which sector 18 isn't too easy to take, cause you'd have to swim there if you want it early in the game).

What poison quest do you mean? The water poisoning or dying fallow trees? I've never been able to avoid the water poisoning quest. Maybe if you took sectors 29 and 30 already on day 2, maybe then that quest wouldn't happen. If you're talking about dying fallow trees quest, then you've simply finished the game too early. I've never had that quest (either I finished the game so quickly, or died trying earlier), but from different guides I've gathered that it'd happen if you haven't taken certain/enough sectors until you reach certain day.

The fallow sappling quest isn't really important in terms of finishing the game, but Brenda would talk about it if you were able to find her stolen scientific journal in sector 12. To find the journal intact, you have to take the sector in a stealthy way or disable the detonator which destroys the safe where the journal is kept. Also, to open the safe, you need either Mike or the passcode, which can be found in three pieces around Metavira.