Formation experience
Every line-up has formation experience and, when its level is low, players may get confused.
Your team acquires more experience points every time they play in both a league or a friendly match. The formation experience grows in proportion to the number of minutes spent in that formations.
Drop after a match update
If you don't play with a certain line-up for some time, the experience in that formation will decrease (it can happen only during one of the two weekly match updates). Also, anytime you sell a player, you slightly risk losing formation experience.
A good idea is to always use an alternative, or switch between at least two alternatives. If you use more than three alternatives it will be difficult to maintain formation experience.
Extreme formations
Concurrently the 4-4-2 is no longer the "standard" formations, so it does not maintains excellent routine. Any legal formation, being no more a subset of 4-4-2, gains formation experience in the same way starting with season 42 (April 2010).
Before the decision to ban extra players (central defenders, inner midfielders, or forwards) and some types of extreme formations, some line-ups couldn't get any experiences. For example, until season 38 (February 2009), national teams and National U20 teams would get formation experience even when using four or more inner midfielders or central defenders, but this was removed just a couple of weeks before the start of the World Cup.