1 It could be that you have been beating Pokemon that gives Attack EVs
2 You could have been using a Item that boost Physical Attack
3 You engage in battle and someone lowers your Sp Atk
4 You engage in battle and someone is boosting your Attack etc Swagger
5 You are just imagining things like you use Water Gun and your physical move is Rock Slide
That's the possibilites I see
You could also use a Reset Bag on your Greninja so you could EV train it in SP Atk