Kate could have touched it when looking out when she found Madeleine missing, if you fake an abduction, you are normally intelligent enough to wipe finger prints off anything that might incriminate you.
There would be nothing at all extraordinary or incriminating about fingerprints from the occupants of Apartment 5a being all over the interior of the window. What is extraordinary is that so few fingerprints belonging to any one were found.
Probably worth noting that the handle would have been used to open the window, an attempt to do so by placing the fingers of one hand on the glass and pushing probably would not have done it and it would have resulted in smearing the prints.
The report states "The fingerprint inspection was only carried out on the inside of the window because it was night time,".
There is no record of the outside of the window or the cill being checked forensically nor does the report mention how many inadequate prints were found.
The report states, "Outside of the external blinds to the children's bedroom: three inadequate prints were recovered." We know that Madeleine's father and others interfered with the "blinds" because they thought they could not be opened from outside, only to discover that they did.
Fingerprints were sent to other countries, "Several prints were unusable for comparison purposes;
all others were compared with no results."
Later one was eliminated, "These were compared to the finger print which was identified as being that of Nelson Filipe Pacheco da Costa of the Lagos GNR."
So it appears that there are fingerprints lifted from the McCann apartment which remain unidentified ... they are not the fingerprints of anyone who had legitimate access to the apartment and until they are identified it leaves the probability that one may belong to a burglar or an abductor.
I believe there are also unidentified hairs lifted from within the apartment;
unknown hairs + unknown fingerprints = unknown person;
so until that unknown person is identified no-one can state that there is no evidence to support Madeleine's abduction.
Quotes from:
http://www.mccannpjfiles.co.uk/PJ/FINGERPRINTS.htm