Are you calling the defensive plays yourself? And if you are, are you relying a lot on the formations the game is telling you the other teams is likely to run? I ask this because it seems you have the most problems during the last minutes of the game or half. A lot of times, the problem is that the offense will go into spread formations with 4 WR's constantly if they are down.
That's fine, and realistic, but the game doesn't take that into account on your side. If you are letting the coordinator call the plays, he's doing it based on normal game situations. In other words, it's basing the play call on what formation the offense would likely use on 1st and 10 at the beginning/middle of the game. The same way with the suggestions when you call your own plays. The game will tell you that they offense is likely to line up in an I-formation with 2 WR's even though the computer in the last few minutes is probably going to go into spread formations with multiple recievers if they are down. The game simply doesn't compensate for the end of the game changing the playstyle of the offense. You wind up covering recievers with LB's because you're in your base defense, and that's just asking to be eaten alive.
If you're holding the offense pretty well until the end of games, this is generally the problem. If you don't call your own defensive plays, take over at the end of the game. Also, ignore whatever the game tells you the offensive formation is going to be. Just play the situation. If the computer is down, call dime packages or similar regardless of what the game tells you.
You won't see great results immediatley though. If you haven't been calling the plays this way, your nickle and dime pakages are going to be way behind everything else in terms of players playbook knowledge. They just don;t get called as often as base defenses. It may take a few games to get that knowledge up, and you'll have to deal with blown assignments until them. But pretty quick, you'll be up to par as far as that is concerned.
Like I said, this is all based on assuming you aren;t calling you own plays or are relying on the game telling you what formation the offense is lining up in. But if that is the case, this should get you going defensively in the last minutes of games within a few weeks.