Player has no concerns yet refuses contract talk because of "his concerns"

I'm afraid it's as the agent says, he may have dropped those concerns, but he still doesn't believe the squad to be strong enough to want to stay. 

So basically everything the game tells you is useless, because the player still can act and think differently? 

I wouldn't say it's useless, but the positives/negatives can be weighted differently. The concern about the ability in the squad outweighs the positives.