I am thinking of taking a trip to Munich from Innsbruck by train. I noticed that there are no afternoon trips. Did I make a wrong search or there is really no train that leaves in the afternoon?
I don't know where you are looking, but the best place to look is on the German Railways website, as it is their tracks and their train: http://www.bahn.de/p_en/view/index.shtml
From 'Innsbruck Hbf', to 'München Hbf' it is showing me trains at 12:36, 12:54, 14:36, 14:54, 15:28, 16:26, 17:05, 18:36, 18:54, etc.
"Did I make a wrong search"
Yes, there are plenty of trains leaving in the afternoon.
Instead of the link above, go directly to this website. The above link will get you here eventually, why not start here.