Did you make absolutely sure that:
a. The EVs totaled no more than 510.
b. Both the ID and the Secret ID are yours.
c. The IVs were realistic, e.g., no 31 IVs in everything. Generally a legitimate Pokemon has no more than two IV values that are 31.
d. The moves were realistic, e.g., no Shiny Swampert with Aeroblast.
e. No banned Pokemon, e.g., no Deoxys in the Battle Tower.
Whether the Pokemon is shiny or not is irrelevant; as long as they look legit, they should be fine.