This thread over at Reddit is from a user who lost their Tengu in a mission and found their own wreck was looted by their MTU which in turn was killed by a fixed emplacement. They include a KM of the MTU loss that only shows NPC damage
I haven't had any situations where I've seen my Mobile Tractor Unit (MTU)being shot by NPC's but then again I have a set target elimination pattern and at the top of that list, after frigate sized ships are sentries and batteries, but it does seem that there is a chance that your MTU could be destroyed by an NPC fixed emplacement.
According to CCP in this devblog, the description of the MTU is as follows:
The Tractor Unit only takes 10 seconds to deploy, and takes up 100m3 of space when stored in cargo. Like the Depot, it can be deployed anywhere away from Gates, Stations and Starbases, which means that it can be deployed inside missions (where NPC pirates are not interested in shooting it), asteroid belts, or on the field of your big fleet battle at the Infrastructure Hub.
I have highlighted the relevant text and it does state that NPC pirates should not be shooting at MTU's. I would include [faction] sentries and [faction] batteries in this, after all they may not be ships but their names clearly indicate they are offensive/defensive emplacements of the faction.
So it seems we need to be a little wary with MTU's and NPC aggression, at least until CCP confirm that this is either a defect or correct behaviour (the former being the frontrunner) and then provide a fix if it is indeed is a defect then all mission runners need to make sure that they do not leave any active fixed emplacements when a MTU is active.