It depends on what sets them apart from what they're meant to shift into.
Examples from folklore and mythology. Werewolves fall into a dozen or more 'lineages'. The Greek Lycanthrope was effectively a man cursed by a god to turn into a wolf. As this was a curse, you can expect that they retained if not human level intelligence, then at least their memories.
Germanic werewolves often took up the mantle of their own volition. Depending on the exact folk tale involved, they either had to drink water from the paw print of a wolf, or they have to wear the pelt of a wolf they killed with their bare hands. This is thus a voluntary change. In the case of 'wearing the pelt', they started out clumsy and their wolf form was just slightly larger and far more aggressive than natural wolves--they also had to hide their wolf pelt, so you could find it and lather it in rock salt to make changing agonizing. In the case drinking from the paw print, they would be almost indistinguishable from a natural wolf, but would have an intelligence in their eyes and used tactics unheard of with natural wolves.
My point here, is that there's something that sets them apart. 376
If you take modern day technology into account, you're apt to find even more differences. Suggestions:
* a higher or lower body temperature than natural creatures
* an imperfect shift (especially with less experienced shifters), where there are some 'abnormalities'. Think wings with abnormally large feathers, or claws that are either misshapen or the wrong length/colour.
* an odd glimmer in their eye, either their iris or their pupil.
* odd body language or sounds considered unnatural to the species. Just because they can shift, doesn't mean they understand the nuances of communicating in their shift's language. Think pigeons that make odd sounds, or dogs that can't communicate with other dogs.
* blood samples. They can shift into the species. Does that mean they carry the species' DNA?
* how does the nanotech that allows them to shift affect them in human form and while shifted? Does it slowly impart bits and pieces of the shift? Rat-shifters slowly starting to hate the light or being able to navigate mazes with relative ease? Dog/wolf-shifters becoming more pack oriented? Perhaps slowly affecting their nails and joints and height and voice?
If you apply scientists attention to detail and the scientific method of dozens if not hundreds of people finding this new avenue of applied science/tech? There's no way they won't find ways to differentiate them. Anything from 'one less bone in their left small toe' (from My Hero Academia) to 'distress markers in their DNA' to 'sensors that detect nano-tech'.
But, that all depends on the specifics of how these things work and what little tells you want to leave in. 802