There is probably a typology of negative trips, but obviously very little science has been done on it. My (inter)personal experiences identify a few distinct culprits, perhaps amongst many, or perhaps all a naive fiction i've constructed for myself:
1. Overstimulation, an inability to cope with all the new perceptions. This is especially pertinent during come-up. If you experience overstimulation in sober life, you'll probably recognize it. If you haven't, it feels like agitation and confusion.
2. Anxiety that is brought into the trip that is either consciously perceived or not beforehand. If something's bothering you at the back of your mind, it's going to come up front and center.
3. Intrusive thoughts. There's no reason why they can't happen on a trip, right? Like sober life, the best thing that makes them go away is acknowledging them and letting them play out. Trying to force them down can make them worse. Intrusive thoughts can lead to disturbing experiences even if they don't result in a bad trip.
4. Panic from feeling your own body in unfamiliar ways. Your proprioception shifts rapidly with LSD. You might not be able to tell where your limbs are, or whether they even still exist. The solidity of your body suddenly feels a little too insubstantial. You can't tell if you're too hot or too cold. Blankets don't seem to work. Come-up can be rough like this. You need to have immense trust in the world that you're ok, that you're not falling apart, that your body can take care of itself and your brain will soon compensate for the new chemical situation and restore homeostasis and understand your modified internal senses.
5. Temporary psychosis. it happens and i am not qualified to suggest a remedy or reasoning to it.
Edit: Sleep! Sleep deprivation is definitely on this list. Can't sleep on acid.