I've seen a few people here and on the Steam forums talking about the issue of having too many fingerprints collected and stored, so many that it makes solving cases too easy.
An idea to help fix this could be for the player to only store fingerprints that have been pinned to the board and when the case is resolved all prints pinned to the board can be wiped/forgotten. This way you can pin as many prints at the scene as you find appropriate so that you can compare them to prints found during the investigation, but you won't be holding on to unnecessary prints after the case concludes.
Seems like this would be an easier balance to implement than making fingerprints more complicated.