I have noticed players go up in wages when i train them. However when i restart the game the wages go back.
that's a glitch

Signed a player that was on 11k wages.
Had full squad so i put up a guy that sold in 2h and i gave the new guy a contract.
Now his wages is 94k...
his 11 K' it's his old wage, before improving in quality.
This could continue if you had him direct in your roster.
94 K' it's the wage of his new quality.

in higher levels doesn't matter as all the players have about same values and wages but in lower levels, it's better to have a 21 players roster before go buying players (from transfer market - recommended and scouts it's the same).