It was a while after the incident with Malfoy, when it was finally figured out how he was able to enter the Common Room, and the girls Dormitory. After lots of research in the Library, Hermione was able to figure it out, as even thought the professors knew, they wouldn't tell anyone, saying, that it must have just been a fluke.
Turns out, that there have been a few cases on record of people who, when they are sleeping, their mind goes to a state where the magic they are able to do then, is much more powerful then when they are awake. None of the people on record have ever been able to control this power inside of them. After telling Harry and Ron about this, they all figured that is what happened, that Malfoy has this other power. They also figured that this power must be strong enough for him to be able to either fool the Fat Lady into believing he is from Gryffindor and has just lost the password, or was able to just know the password. Also, that he must have been able to get into the girls dormitory by using this power.