I'm playing through the game again trying not to kill anyone or be spotted in order to get the clean hands and ghost achievement. For some reason, every time I enter the room with all of the plant monsters before entering the outside area before you get to Daud's base, I keep hearing the alert sound. I'm not seeing anyone who can visibly see me but for some reason I keep hearing the sound and I don't wan't to continue to beat the level and not realize that I was actually spotted. This is frustrating, can someone help?

i think the plants do count as alerts, that's got to be the only thing ruining me on that lvl.

Plants don't count toward your detection.

Are you sure it's not just a scare/warning cue? Like, a sound that indicates, Oh no, here comes the zombie! Or, Oh no, here are lethal venus flytraps slash mollusks!

Maybe a weeper on a balcony?

O.O Oh great now they are ontop of roofs. This game....is not forgiving

Is that the room with an open roof, with a lot of Overseer's corpses? And you can open a door using a big valve? Are you n the way back from recovering your gear and to Daud's base?

First, there now are some assassin's on the roofs there. Notably on the roof next to the building you're in. This one has a patrol which bring him to a spot where he kneel and look right into the room. So if you're still there, it's possible he spotted you.
Second, opening the door with the valve will, as hinted by a note near a dead overseer's corpse, attract one assassin who will first observe the bridge, and then if no one comes out, walk to the valve.
Third, there indeed is a weeper in a room a bit further, where you can find a Sokolov's painting. Maybe he saw you. That's unlikely though...
Fourth, nah, the River Krusts do not count as detecting you so it's either an assassin or a weeper

I only did the game in a low chaos setting, maybe there is more thing to be aware of in high chaos...