The difference between those three players and Fred is that they were good enough defensively to play that screening role in front of the defence by themselves. Fred isn't, because he's better at pressing than sitting deep and doesn't have their positional sense.
Fred gets the ball enough in threatening positions for his atrocious shooting and so-so decision-making to be a problem, and he's not defensively secure enough to make up for it. No one would be complaining about his shooting if he was shielding the defence like prime Makelele.
No matter how people rate his defensive work, I still think that rating his shooting is irrelevant to his position. If he was so good at shooting, you would have to question why he is even playing as a defensive midfielder in the first place; their chances will mostly be low Xg from distance. Looking at his goals at Shaktar, most of them actually came from inside the box.
His defensive work is pretty good, anyway. He made our third most tackles per game last season, after Wan Bissaka and Matic, and has made our second most tackles per game this season after Wan Bissaka. (2.1 last season; 2.7 this one).
In terms of interceptions per game, he was fourth last season with Mensah (albeit, he didn't play many games), Bissaka, and Maguire ahead of him. This season, he is third with Maguire and Mensah (played 1 game) above him (1.3 last season; 1.6 this one). So, on average he dispossesses the opposition 4.3 times per game (when you add tackles and interceptions), which is only beaten by Wan Bissaka who wins it 4.4 per game. Fred has also improved defensively on last season.
In comparison to other DMs, his dribbled past stats aren't all that different from others in the league. Allan gets dribbled past the most (2.5); Fred (2.1) is similar to Romeu (2), with Hojbjerg (1.8) being slightly better. Kante is the best (1.4).
Allan makes the most tackles per game with 3.4, Kante (2.9), Hojbjerg (2.9), Phillips (2.9), Fred (2.7) - Not much different really, other than Allan.
Interceptions - Kante (2.3), Rice (2.1), Neves (1.6), Jorginho (1.6), Fred (1.6)
Total tackles & Interceptions - Kante (5.2), Romeu (5), Phillips (4.5), Allan (4.4), Fred (4.3), Hojbjerg (4.2). Not really a huge amount of difference between Allan, Fred, Hojbjerg, and Phillips in terms of defending.
Fred actually seems to be pretty well rounded. Kante and Romeu are the best all-round, while other DMs seem to be distinctively better at either tackling or intercepting. Allan seems to be the best tackler, but interceptions seem low (only 1 per game).