I appreciate you answering my question Shorty69. I finally resolved the problem on the mission MADSEN UNDER ATTACK. I found someone on the internet who helped me. Here is what you do:

Step1: When you are Chase Edmunds go up the water tower and press pause and save the level. The clock should be at 4:08, save the game from this point. Step 2. When you have saved the game restart your PS2
Step 3. Load the level again.
Step 4. When the movie trailer comes on with Jack and Tony, take out your memory card and it will ask you for autosave. Press yes to accept autosave and continue watching the trailer.
Step 5: This should solve the glitch. If there is still one man in the main building where the truck is rammed in, that means the glitch is still there. NOTICE: in the PDA it says to kill all guys in warehouse. With the glitch there is only one. If you kill him, that does not beat the level.
Try to do the steps above and you should beat the level with more bad guys making their way inside the warehouse. This worked for me. Good Luck.
Please feel free to ask me any questions if anyone is stuck, I already have beaten the game.

I have made a little discovery about Accuracy, Accuracy determines how good you are aiming and firing your weapon, if you shoot enemies your accuracy increases, make sure none of the bullets miss, if you fire at other things such as Objects, Windows, Security Alarms, Vehicles, Explosive Barrels etc, your Accuracy will decrese sometimes your accuracy will disappear all together. The best weapons to use for increasing your accuracy are the pistol, silencer psitol and the sniper rifle, they fir 1 bullet at a time, to get good accuracy your aiming must be good, if you shoot an enemy in the head, your accuracy will increase. Also you can increase your accuracy from how far away you shoot, the sniper rifle is the key to increasing accuracy. The Clock Is Ticking so try and use these accuracy skills a bit quicker to achieve bonuses

If you want to blow up any vehicle, simply aim your gun at the fuel tank and fire away, it is useful to take out your enemies,
Happy Hunting

Please go to the options menu press and hold L1 L2 R1 R2 and click video then audio and a screen will pop up press and hold triangle and there is invulnerable all missions all bonuses infinite ammo here are the codes.

invulnerable 66BAUER
INFINITE AMMO 62ALMEIDA
ALL MISSIONS 72DESSLER
ALL BONUSES54PALMER