Could they vet have missed something?

hi, i got a puppy 4 days ago he has had the runs since we got him. hes is on wet and dry mixed puppy food the same since i got him. i dont know what he was on before he was a recsue. well i took him to the vet 2 days ago to see if he had worms .. they took a sample there and looked there and said he was free from parasites. anyway could they have missed something like gairdia . he is still pooing like this only once a day .