Yes, the individuals of a species might have phenotypic differences when compared to individuals of the same species for many generations, it is evolution.
Evolution can be defined as descendant having phenotypic inheritable modifications, which generally happen due to the process of natural selection.
Natural selection 'selects' the most adapted phenotypes for a given environment to form the next generation, thereby populations change (evolve) across generations.
In conclusion, the individuals of a species might have phenotypic differences when compared to individuals of the same species for many generations because it is evolution.
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