I have a few issues with extensions.
1. When offering an extension to a coach with a year left on his contract, he accepts it but it disappears when the new season begins.
2. When offering extensions to players, if they haven't signed by the end of the regular season, there is no further action on the contracts... no messages from agents, no signing, no nothing, but you can still go to the player's card and see there is an active offer.
3. When you click on Player Wishes and a contract value comes up... many times the player won't sign. This doesn't make sense if they player wishes 1.5 million for 4 years, you offer it to him, and then he says no. The Player Wishes SHOULD give you an offer the player will 100% accept.
As I'm new in the game, I don't know how similar or different these issues are to the ones you were having in 3.0.2... but these are issues I'm having in 3.0.7.