Hi all,
Been playing my current game (as a fairy) for a while now, mastered a few skills, including science. Have been able to clone any plant from a sample without issue. My sim just came back from China and I wanted to prepare potent invigorating elixir in preparation for her next trip. Had growing glowing mushrooms, so forced bloom with magic and then analysed a few times so I could clone, as I've done before (including in this game before trip). Click on science machine -> clone sample, but none of my plant samples (had all sorts including lettuce, tomatoes, all sorts of beans and mushrooms, wolfsbane and others) appear on the list! Fish, bugs and minerals all there. So tried directly from inventory, where I got this:

I've exited without saving a couple of times now, deleted all my plant samples and analysed a mushroom again (existing one from inventory this time), but one sample was still 'too large'.
Searched endlessly for answers online but have found nothing.
Does anyone have any idea what's going on???
If I can't figure it out I'm gonna have to restart this game, it bugs me that much, so any advice is welcome!
Thanks.

Since you mention your sim traveling to china, are you using the default EA story progression? Many issues are caused when your sim travels, because Story Progression fails to handle many situations properly. You may want to have a look at Nraas http://nraas.wikispaces.com for a Story Progression replacement, and perhaps also get MasterController and Overwatch. It may be that your sim is just glitched somehow and you'll be able to correct it and free them up.

Hm, I don't think that I was ever able to clone a mushroom or some other specific harvestables that are considered "too large". Are you sure that you've cloned mushrooms before?
But as regards the other "ordinary" harvestable samples, did you have them travel with you to China and back? I know that travelling breaks uncut gems and unsmelted metals (they revert to a default appearance and often refuse to stack), maybe something similar happens to plant samples.

Same issue, nraas story progression master controller and overwatch werent the fix, I was able to clone them at some time; but now i cant

I was able to do plant cloning back then without traveller mod. Perhaps try to erase all the plants in your home lot, and replant them. If it still doesn't help, use reset everything command with master controller.

Thanks for the suggestion, I've deleted every plant from my lot, sold every plant in my inventory and went to the alchemy meister's to get new ones. ones i bought didnt work as well, and the one i planted didnt work either; also I've already tried resetting town sadly no good results. By the way, I dont have any problems with normal harvestables, it seems like it's just alchemy plants like Wolfsbane, red toadstool, red valerian etc

Maybe there's a bug or something with supernatural harvestables since I only cloned ones from base game and university life. I am using a no ingredient needed for alchemy mod so I don't need to plant every alchemical seed.

I realize this is 10 years old now but I am willing to necro this on purpose for anyone in the future who will still need help with this issue since this was never solved.
I just recently found out how to work around this, however I could not find much on the internet about it.
The trick is to not click on the item in your inventory, but to do it from the machine, which gets you a list of possible things to clone. There however you wont get any alchemy related plants selectable.
In order to have stuff like mandrake etc. listed there you need to have the stack of plant samples in your inventory start with an item that is cloneable, like an apple, or any other cloneable plant.
Go in that stack of plant samples in your inventory and move all the mandrake, and other alchemy samples out / to another sim and then put them back in at the end of that stack.
So that they end up down in the stack.
If you now click on the machine and select clone from sample you will get that list of items, but this time it will have the alchemy stuff (like mandrake, wolfbane etc.) selectable and you can clone regardless of size.
This is possibly also the reason why it worked at the beginning, depending on how that stack looked like back then (with a clonable sample at the front) and if you used to click on the machine instead.
It is probably only working now due to a glitch and sloppy programming of EA