Pokérus has a random chance of spreading to adjacent Pokémon after a battle. If you have Pokémon with Pokérus in the Second slot and the Fifth slot, it will spread to all of your party, within a few battles. Placing Pokémon in the box doesn't spread Pokérus, it preserves the 'active' state of the virus (when it can spread), so keep some in your box. When your Pokémon has been in your party for around 1 day, it will revert to the 'inactive' state, where it cannot spread however it gives the x2 EV still. To answer your question, no it isn't, it is simply bad luck.
Source: Knowledge and this
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