When Paul puts blood in the water system, he tells Maddie some "animals got in the septic system." He knew well the difference between the water supply and the septic system (as most people would). It would be a key error for him to say what he said as it would be too likely that anyone would know he was lying.
When Paul rigged the bathroom door knob so that it would come off in Maddie's hand, the camera showed him working on the latch portion of the system. There is no way a person can affect the door knob by working on the latch. Also, the knob portion would have contained more of the mechanism and she would have been able to open it fairly easily.
Near the end, when Maddie was talking to 911, she was talking on a cell phone and cell phones had not worked in the house throughout the movie -- no reception. If she had simply been shown talking on the landline, there would have been no continuity error.