I don't think they have a clue just what is going on. I have a 2014 with 83,000 miles. They replaced the complete engine 5,000 miles ago after the same situation you discribed above happened eight times from July 2016 thru May 2017. Prior to that, they had replaced the turbo sendor, the complete turbo, several injectors at different times. I don't believe changing out the fuel filter any sooner would've helped. I change mine out when I do an oil change, which is just less than every 10,000 miles.
The dealer had a Chrysler engineer fly in to do the evaluation on the engine prior to being replaced. The engineer was here all week doing all kinds of diagnostics; truck was at the dealer for about three weeks during this time. The dealer said the engineer told them this seems to be an epidemic across the country with this engine. To date, since the introduction of this motor, the dealership that did the work has replaced three ecodiesel engines, two because of lower bearing failure - these were just lower engine replcement, and one complete engine (mine) injectors and all - service manager said that is not normal to be replacing so many engines. And they are just one dealership!
You are definitely making me want to go back to a gas engine, at least until they figure out what is going on with this engine. Really unfortunate they don't have all the bugs worked out. Too many EPA requirements I think.