It's not just teamwork that's the problem, it's the team's overall structure. Let's imagine a full 16 player team on cp_steel, BLU team

5 Scouts
0 Soldiers
1 Pyro
0 Demos
2 Heavies
1 Engineer
1 Medic
3 Snipers
3 Spies

Do you see the problem with the structure of this team? There's no push present. If the five Scouts are rushing E for a "fast" win, that leaves a team of 11 against a team of 16 defending A. All the Snipers are too busy sitting in spawn, the Medic is overworked because he has to constantly switch between Heavies and the Pyro, the Engineer is building a teleport that goes close to E, the Pyro is trying to Spycheck on his own, and the Spies are mostly fail spies who can't even break the top 5 on the scoreboard. The other team was something like this.

1 Scout
1 Soldier
2 Pyros
2 Demos
2 Heavies
2 Engineers
3 Medics
2 Snipers
1 Spy

This presents us with the frequent problem, players on the losing team claiming that teams are stacked. The teams are only stacked in your mind, the real problem is the other team has better structure and functions together.

TL;DR Stacking is all in your head

(Yeah, this isn't going to make sense and people will think I'm insane for typing that, but it's how I feel.)