He hit him plenty of times on the chin, so he may have. Mosley worked the body more than Cotto did though and I think that attributed to him getting knocked out too.
If Margarito was softened up by the Mosley fight I'd attribute it to all those years of pro fighting with a high energy style and a below-average defense, rather than just looking at Cotto.
Cotto hit Margarito with everything.
http://i294.photobucket.com/albums/mm96/cortes9979/Untitled-4.jpg
It's funny that Margarito looks worse against Cotto, but obviously took a bigger beating in the Mosley fight. When you hit someone in the jaw it often times doesn't leave marks on the face but it will KO you a lot quicker.