If you are referring to the mission where you have to recover a med-kit for a colleague first?
This mission is notoriously bugged, you must not kill anyone in the first part (daytime) except for the soldiers near the little farmstead away from the base, also do not let anyone see you even for the slightest moment.
At the start of the game (daytime) as you head up the road past the entrance, there is a bug where, near the entrance, a soldier goes "alert" for no obvious reason when you are in cover or nearby, he does however, not chase you, simply runs towards the bushes, along the road and back to the entrance.
Regardless, if he goes alert you will never complete the second (night-time) part of the mission, so you'll have to restart.
If you get to the second part of the mission at night without alerting anyone, you will have to refrain from being seen or harming anyone again (you'll be told when you can) so once again check whilst playing for rogue soldiers going "alert" for no reason
The bug is believed to be caused by the offending "alerted" soldiers being able to see through cover and buildings to you to become aware of your presence, you can minimise the chances of being seen by performing the whole mission with your troops crawling, which sadly takes an age to do but means you don't have to restart.
As a final note, when clearing the farmstead away from the base, two soldiers come from the road to the base, make sure they are both killed or one will run back and "alert" the base without you noticing.
I wrote about this over at the DigitalMind forums will edit this post to add the URL if i dig up the link
Regards
Jacob
[Edited by JacobD88, 8/5/2009 5:02:38 AM]
[Edited by JacobD88, 8/5/2009 5:03:42 AM]