Just rest them for a game and it won't effect their match fitness noticeably. I would rest them unless it is a must win game and I had a week before the next game to allow them to recover. They will be more likely to get injured if they play too many games when they are below 95%.
There could be several issues. Tough to say really. They might just need to play more. You might need to adjust training schedules. You might need to invest in a better fitness coach.
On my team, the back half of the bench are usually not match fit. I don't worry about it. If I need them, I play them anyway and haven't noticed any problems in doing so. I only concern myself with the fitness/condition of starters and the top few bench players. The rest of the squad just has to play when I tell them to play.
I've had some success in tweaking 'Strength' and 'Aerobic' up a bit. I like the 'Strength' parameter to stay at 'High' ( lowest point - after 'Medium' ) and the same for Aerobic, if the players can manage it without getting injured. Watch also the 'Overview'-option carefully. Maybe they even can tolerate tougher 'Strength' and 'Aerobic' intensity.
I've experienced in many cases that this can get them up to 100% match fitness, when they earlier have struggle to reach this point.