How did he climb up the wall and break in and not show any evidence by the windowsill, like fibers from his clothes, handprints, nothing. Why is the glass on top of the things? How did the murder scene get contained to only Meredith's room? How did he know automatically know the door was locked? If he did not automatically know, how comes there are no footprints going back and forth from door to purse and back to door? Where are his missing footprints? Where is the blood from locking the doors? Why would he lock Meredith's door but leave front door unlocked? How did he restrain Meredith and attack her at the same time, to account for the what the evidence shows? How was he in the bathroom and there is no evidence of him in there, blood-wise? If he wasn't in there, how did the smears/blood get in the bathroom yet in such a relatively small amount to what would have been on Rudy? Where are the missing footprints going to the bathroom? Why the overkill? Why use a knife when he could have killed her in a less messy way (such as strangiing her?)? Why choose the messiest way possible? Why is the scene outside of the bedroom so relatively clean? Why didn't he also check Laura and Amanda's room for things to steal? Why only Filomena room and Meredith room? If he was already in the house when Meredith came in, why didn't she notice the broken window or Rudy in the bathroom, there must have been a light or two on for him to get to the bathroom or wherever he was going? If he was so calm about using a bathroom, acting like he wasn't worried if someone walked in, why wouldn't he turn on the lights? And if the lights were on, why wouldn't Meredith notice? Why woudl she walk all the way to her room first??
That is just off the top of my head.....