you need to build up the stamina of your players, they're most likely running out of steam late on and are getting sloppy, also try to bring on players with high determination, they'll fight to hold onto the lead better than those with a low rating in that stat.
Definitely agree with boozemaster. Tired minds and tired legs make for late goals. Consider how you're pressing throughout the match if this is becoming a major problem - too much and you're guaranteed to leak late goals as your players will be knackered.