Maybe he is putting it too far? I have taken 3 small dogs to my vet and they have done fecal tests several times and mine don't really notice that they had something in their little butts! Now I just have two.They actually just did that fecal test on Cookie This week and he didn't even blink an eye. Maybe you should tell your vet of your concerns regarding this? I know some vets might get mad and tell you that they are experienced and know what they are doing and some will be considerate and might admit that maybe your furbaby is too small and they might have hurt him a bit
Genie, Cookie & Lola