I would not lift it out of the soil just give it a gentle tug using some kind of grabbing tool. You should no immediately if there is any resistance if there is it has roots, if not at all, then it is still very much rooting in.
Those spots look like some kind of fungal - so moisture related - outbreak, which can happen to plants like this when they are not used to much humidity at all or it is really hot and all of a sudden humid...
Spraying with antifungals will help, but other than that I'd keep an eye on it but would not be too concerned. The plant in the OP you want to keep a sharp eye on the tip if it gets worse you will want to lift it out of the soil and probably decapitate it, but for now it may just pull through. It will probably not grow from that tip, but may branch there.
