Were any species of dinosaurs, other prehistoric reptiles or prehistoric amphibians thought to have been poisonous, and if so, how could scientists arrive at this conclusion with only fossils to work with?
There is some evidence that at least one species of dinosaur may have been venomous, based on a single theropod tooth with a groove similar to that found in venomous snakes. But this is far from being solid evidence.
See here
A distinction is sometimes made between venomous animals, which inject a toxin into a prey or enemy, and those which are poisonous, and contain toxins within the body tissues themselves. It would be possible to identify venomous animals from fossils if the structures that injected the toxins were made of materials hard enough to fossilize. It would probably not be possible to identify animals that were merely poisonous.
In the Jurassic Park novels, it was speculated that some flesh-eating dinosaurs weren’t venomous in the sense of actually secreting poison; but that their mouths and teeth retained so much rotting leftover meat that their bites were highly septic. Modern Komodo dragons have this feature.
As do wolves, vultures and almost any other animal that eats carrion, whether they have teeth or not. The evidence that this is anything but accidental and that it plays any role whatsoever in prey capture is non-existent. That animals like vultures, that almost never take live prey, have the same basic oral flora as predators suggests that it is entirely accidental and in no way equivalent to venom.
Flora or fauna?
Flora. Microbiology used to be a branch of botany and retains alot of the same nomenclature.
Microbiota. 
In the first JP book (and the movie), the dilophosaurus had a very acidic saliva which they spit into the eyes of their prey, which was how Nedry the Corrupt Programmer was killed & eaten. Also in the book (but not the movie), the procompsognathids injected a soporific into their prey, which was how they ganged up on and ate Hammond.
Right, but that was completely made up.
However, I think it is entirely appropriate for an author of a work of fiction to make stuff up like that. We only know a limited amount about dinosaurs for sure, because we only know about things that were fossilized. But we know for sure that all animals traits that wouldn’t be preserved by fossilization.
So all we can say for sure is that if we had real-life dinosaurs to study they’d have suprising traits that we’d never have been able to discover through their fossils. Meaning, we’re guaranteed to be surprised. So a book about real-life dinosaurs where the dinosaurs don’t have surprising traits would be completely unrealistic. So to be realistic you are pretty much obliged to throw in random weird stuff that you have no reason to suspect would be true in real life. If that makes any sense.
Stupid sorta related question. Could the dinosaurs have been red/purple/pink with dots, not saying they where but is there a way for us to know through the fossil record? As you can probably tell I am pretty dumb on fossils, and all that.
There’s no real way of knowing what colour most fossilised animal were. Some animals derive their colouration from refraction and the refractive patterns can be preserved by fossilisation so we can get a glimpse of the colour of some animals like butterflies in that way. That’s almost impossible with dinosaurs because the skin is so rarely preserved. AFAIK nobody has managed to recover any refractive material from dinosaurs, so we’re just guessing when it comes to colour.
Could they have been red/purple/pink with dots? It would be surprising if many of them weren’t. These animals were closely related to birds and it would astounding if they didn’t develop the same colouration as birds. Lacking feathers they may not have been quite as showy, but purple, red, pink and blue wattles are common amongst birds so it’s highly plausible at least some dinosaurs had similar colouration.
And even featherless reptiles can be pretty brilliantly colored…stripes, splotches, you name it. Yeah, your typical lizard is greeny-browny-gray, but lots and lots of them aren’t. So although we have absolutely no idea what color or color pattern dinosaurs were, we have no reason to believe most of them were greeny-browny-gray.
Even if we restrict potential colors to modern reptiles and birds, they could have been black, gray, white, brown, pink, red, orange, yellow, green, blue, or purple, or any shade in between and in any combination you can think of. Of course, any particular imagined color scheme is wildly unlikely, but that greeny-browny-gray is therefore also unlikely. So any color you assign to your dinosaur reconstruction is sure to be wrong, but they had to have been SOME color.
Along those same lines…IIRC, the Jurassic Park sequel book had a chameleon-o-saur, which would’ve been a cool addition to the movie.