What settings were you using? I don't think focus is your issue it looks more like a product of slow shutter speed. Shooting pets is hard enough, let alone indoors. Push the ISO up to around 800 and raise your shutter speed to anything over 1/200 and you should be right.

If you're using Canon make sure that you have AI Servo on (in the focusing options) as this will help track the animals too.

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Ryan