A version of the species list that has official species identifications and identifications for uncertain species that I think (and in a few cases fear) may be official; please don't hurt me over this.
The odds of the producers and creature designers caring about identifying the animals on a specific level are low, so specific names have been ommitted from this list.
Ornithischia[]
Dryosaurus, Othnielia (variant 1?) or Parksosaurus (variant 1?)
Hypsilophodon (variant 1?)
Hypsilophodon (variant 2?), Othnielia (variant 2?) or Parksosaurus (variant 2?)
Dryosaurus (variant 3?), Parksosaurus (variant 3?) or Pisanosaurus
Pachycephalosauridae[]
Goyocephale, Prenocephale or Stegoceras
Pachycephalosaurus (variant 1)
Pachycephalosaurus (variant 2)
Ceratopsia[]
Chasmosaurus
Microceratus or Leptoceratops
Pachyrhinosaurus
Styracosaurus
Triceratops (variant 1)
Triceratops (variant 2)
Ornithopoda[]
Iguanodon (variant 1, the one with the horn on its nose)
Iguanodon (variant 2)
Muttaburrasaurus
Ouranosaurus
Hadrosauridae[]
Anatosaurus (variant 1)/Parasaurolophus (variant 1)/Saurolophus
Anatosaurus (variant 2)
Corythosaurus (variant 1???)
Corythosaurus (variant 2?)
Edmontosaurus, Hadrosaurus or Kritosaurus (the fat-beaked dude on the right)
Lambeosaurus
Maiasaura (variant 1)
Maiasaura (variant 2)
Parasaurolophus (variant 2, the one on the right)
Parasaurolophus (variant 3)
Parasaurolophus (variant 4)
Thyreophora[]
Ankylosauria[]
Ankylosaurus (variant 1)
Ankylosaurus (variant 2)
Ankylosaurus (variant 3)
Euoplocephalus
Nodosaurus (variant 1)
Nodosaurus (variant 2, the white and gray nodosaur)
Stegosauria[]
Kentrosaurus
Stegosaurus
Theropoda[]
Allosaurus (variant 2) (based off of comments from a JotB storyboard artist) or Yutyrannus (based off of the design)
Baryonyx or Suchomimus
Carnotaurus
Megalosaurus??? (the blue one that's yawning)
Spinosaurus
Carnosauria[]
Acrocanthosaurus
Allosaurus (variant 1?)
Neovenator
Coelurosauria[]
Coelurus
Compsognathus (the little blue thing, not the big brown thing, variant 1)
Compsognathus (variant 2)
Compsognathus (variant 3)
Tyrannosauridae[]
Tyrannosaurus rex (variant 1)
Tyrannosaurus rex (variant 2)
Tyrannosaurus rex (variant 3)
Tyrannosaurus rex (variant 4)
Ornithomimosauria[]
Dromiceiomimus
ID'ed as Ornithomimus (variant 1) (ID'ed as such in some production material, may have been changed to Struthiomimus later on but there is no good evidence for this)
Ornithomimus (variant 2) or Struthiomimus (variant 2)
Struthiomimus (variant 1)
Struthiomimus (variant 3)
Maniraptora[]
Archaeopteryx (variant 1, bird thing on the top right)
Archaeopteryx (variant 2)
Beipiaosaurus
Deinonychus (variant 1)
Deinonychus (variant 2)
Dromaeosaurus
Ichthyornis
Microraptor
Nothronychus
Oviraptor
Velociraptor (variant 1)
Velociraptor (variant 2)
Velociraptor (variant 3)
Sauropoda[]
includes some traditional "prosauropods", bear with me
Argentinosaurus or Seismosaurus (back left)
Plateosaurus
Tinysaurus (all but the big one)
Diplodocoidea[]
Amargasaurus
Apatosaurus (variant 1)
Apatosaurus (variant 2)
Apatosaurus (variant 3)
Apatosaurus (variant 4)
Diplodocus (variant 1)
Diplodocus (variant 2)
Diplodocus (variant 3), Mamenchisaurus is a distant possibility
Diplodocus (variant 4)
Paralititan?
Supersaurus
"Ultrasauros" (left)
Macronaria[]
Brachiosaurus (variant 1)
Brachiosaurus (variant 2)
Brachiosaurus (variant 3)
Camarasaurus (in front of Sue, variant 1 / male?)
Camarasaurus (the one on the left, closer to the bottom of the screen, variant 2 / female?)
Saltasaurus
Non-dinosaurs[]
Pterosauria[]
Cearadactylus (variant 1)
Cearadactylus (variant 2)
Dimorphodon (the fuzzy ones)
Pteranodon (variant 1)/Pterodactylus (variant 1)
Pteranodon (variant 2)
Pteranodon (variant 3)
Pteranodon (variant 4)
Pteranodon (variant 5)
Pterodactylus (variant 2)
Quetzalcoatlus (variant 1)
Quetzalcoatlus (variant 2)
Rhamphorhynchus (variant 1)
Rhamphorhynchus (variant 2)
Suchia[]
Deinosuchus (variant 1)
Deinosuchus (variant 2)
Deinosuchus (variant 3)
Marine reptiles[]
marine reptiles in general, no groups or anything like that
Dragon thing
Elasmosaurus (variant 1)
Elasmosaurus (variant 2)
Kronosaurus
Liopleurodon
Ophthalmosaurus
Plotosaurus
Other reptiles in general[]
ignoring the nothing lizards from Littlefoot's birth
Archelon
Lizard
Longisquama
Probably didn't have an ounce of thought put into what it is
Really big snapping turtle
Tortoise
Turtle
Synapsids[]
Ceratogaulus
Didelphodon
Dimetrodon (the saily guys, variant 1)
Dimetrodon (variant 2)
Mouse
Rat (variant 1)
Rat (variant 2)
Amphibians/basal tetrapods[]
Euparkeria
Frog (variant 1)
Frogs (variant 2)
Ichthyostega
Salamander
Fish[]
Barracuda
White shark
Pike