well, chemistry has a lot of forms in T11
Some are obvious, for example as @woopypooky said or we must discover them.
A pair of wingers or DCs is working better than another
A DL-DC perform better in the DL position than THE dc
One player has more "talent" in corners than a specialist we bought this season.
Our defense/counters works better if we have less b.p.
A player who was low 6* and now low 5* (or maybe 4*) some times is more guarantee in performance than a new 6* player.
Some high q players (from scout or recommended) play better in their second season
Some teams have a weird formation (unbalanced) but for some reasons it works.
Some are more hidden, for example
I had a T11 friend who was buying every second season 12-13 scout list players (the old times, before recommended).
He had a super team but couldn't win so much titles as my team which had young nordgens with a lot of training.
Maybe there is a hidden factor (a penalty) which affect the team's performance.
Some players perform better in specific competitions.
A 5* player can play better in the Cup than a 6-7* but not so good in CH.L.
Later in the season, we can observe some stats.
There was an old forum member who said that as the whole squad is training together, that increase the in-game performance - don't know about that.