I cut out some clones off my mother plant today and put them in a bottle. In the bottle, I put a fogger in there and left it alone for about an hour because it seemed as it was working nicely. When i came back to check on it, the water was boiling hot. the clones aren't touching the hot water, but it was chilling on the fog it made. the stem where the roots are suppose to come out of is very weak and flat right now. will my clones be ok?

mine uses a fogger and they've turned out fine.

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I wouldnt think so mate id say if the bottoms have gone soft anuff just to be flat id say they are dead as same if you keep cutting medium to wet they will rot and go flat and soft just stick clones in a humidity dome at about 27 - 30c and see what happens and keep ya fingers crossed or if you got room on the cutting try operate on it lol amputate

the leaves have turned to the light, does this mean that it's still alive? the bottom of the stem is still weak and flat

how many leaves your clone got mate
and if it responding it still alive else it would wilt
and die
idealy you want 2 leaves and a grow node in your medium
and have you just left the fan leaves or cut them in half or chopped fully off
as you dont want the leaves using all the plants goodness
and will help root faster ive found if i chop the leaves in half