The obvious that comes to mind is that the contamination most likely occurred by touch transfer during one of the many sloppy searches and rummagings.
I think the "133 samples" argument is misleading and distorts the truth. The important information that it omits is:
How many of those samples gave no results because of incorrect collection/storage/testing?
What was the distribution of those samples and how does it correlate with the areas and items where we would expect to find Raffaele's DNA?
We already know that most of those 133 represent traces taken from exhibits collected in Meredith's room.
We also know that of the few times he was in the cottage, most of the time Raffaele spent in the common area. He cooked and ate in the kitchen and most probably washed hands in the adjacent bathroom. On the morning after the murder he looked around the rooms and tried to force Meredith's door.
Where do we expect to find his DNA? First - On the things he touched - kitchen utensils, bathroom faucet, doors, door handles,
ETA: the refrigerator 
. Second - on the used clothing and underwear that Amanda left in her room.
Was any of those sampled for DNA?
Lets take for example the kitchen/living-room. According to the index of evidence only the cigarette butts and samples of presumed blood from the floor were collected.
From the large bathroom - only the feces, dirty toilet paper and contents of the washing machine.
From Amanda's room - again "presumed blood" from various surfaces plus a pair of socks (!).
Basically, the things they decided to test outside of the murder room were very unlikely to have Raffaele's DNA and there were things they left behind that very likely had his DNA.