When a player is assigned to play in a strange position to himself, the chemistry is strongly affected. Independently of his connections with team mates, he will never have more than an individual chemistry of 4, which is very bad. However, it will also affect team chemistry.
If you bought or received a player with a different position from the one that he will play, apply him a position card in order to at least adapt him to a similar position (see the table of similar positions).