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This is a legitimate concern and has been addressed to some degree in some areas. Unfortunately we don't have a perfect way of knowing that a specific specimen is from a specific species. Two very similar skeletons could be from the same or closely related species. The same goes for development over the life history of a specific organism. Adult humans have a different skull to height ratio to babies, but the ratio between toddlers and young chimps is very similar.
Fortunately we have many different aged animals of the same species in the same context to compare. We can see the infant, child, adolescent, adult, and aged forms for many species and this acts similarly to transitional fossils, they help close the gap. We can be more sure with more hints like sharing a space, being buried in the same context, having the same nitrogen isotope ratios in teeth, and eating the same prey. Lots of other things can act as clues to the relationships and make us more or less certain of a given relationship.
That said, fossilisation is rare. Not all that many individuals will be fossilised. Different types of tissue fossilise to different degrees and in some cases not at all. If an animal is mostly spongy material they may degrade too fast to fossilise and preserve structure. Other examples may only leave their imprint as a hollow or pressing of one material into another. I think the record is very sparse and will remain so, but adding more example allows more connection and conclusions to be made.