There are certainly a lot of things that happened that whilst they may not be evidence to convict are enough to allow doubts of innocence. If Meredith Kercher's family are concerned about the acquittals then that is completely understandable in view of what has happened. I have taken the following from here:

The Italian appeals process offers more guarantees to defendants than any other legal system in the world, whereby only the weakest evidence is treated, not the whole case. Knox's team only had to attack the DNA evidence against her to undermine the whole edifice of the original trial. Italy has one of lowest prison populations in the world because of its lenient appeals process.

If the prosecution decide to appeal against the acquittals will the two of them be obliged to return to Perugia? Raffaele Sollecito would seem to be at a distinct disadvantage if that does happen since he lives in Italy.