There are a number of things still unanswered from the Silence storyline. Large questions as well as throwaway statements suggesting some connection with a detail from a previous episode that never gets revisited.
I encourage posing additional unresolved plot points, but I'm going to start it out with this:
In Season 6's "Day Of The Moon", The Doctor et al. show up to rescue Flesh Amy from The Silence after she is kidnapped from the orphanage.
When they step out of the Tardis, The Doctor calls our attention to the ship's resemblance to the stranded spaceship posing as a second floor flat in Season 5's "The Lodger":
"Oh. Interesting. I've seen one of these before. Abandoned. I wonder how that happened."
I didn't notice until recently while rewatching what his last sentence suggests. It was the same technology, so it must have been a Silence ship.
How, why & when was the ship abandoned?