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Possibilities many for cause of problem. When I handle repeatedly, which I do alot with birds being trained for some purpose, chick and my hands stay within confines of brooder. Also when picking them up, let them stand on your hand versus holding them like puppy or kitten. Even as they mature, if possible let them stand on you as it is less stressfull.
I have integrated little bitties with age differences as you are considering. Outcome very much a function of breeds involved. If possible, then at time of introduction hand feed all birds in brooder with meal worms and move waterers and feeders to new locations. Will distract larger chicks from new comer and hopefully get them to bond while chasing same morsels.