We found that ultraprocessed foods contain a substantially higher percent of calories from carbohydrates and added sugars, and higher levels of sodium, but also had less fiber and a lower percentage of calories from protein
Considering the vast majority of Americans get enough protein, I'm not sure why this specific observation is considered bad. Calories from carbohydrates (including sugar) aren't intrinsically worse than calories from protein. That's not to say most ultraprocessed foods are healthy, just that the observation doesn't imply they aren't.
For comparison, here's what the CDC has to say about added sugar[1]:
Added sugars contribute calories to your diet, but no essential nutrients. Eating and drinking too many added sugars makes it difficult to achieve a healthy eating pattern without taking in too many calories.
The important thing is that ultraprocessed foods tend to have less micronutrients and encourage eating too many calories.
[1] https://www.cdc.gov/healthyweight/healthy_eating/sugar.html