The new ROE (Rules of Engagement) in Afghanistan stipulate that, whenever possible, Afghan soldiers or police take the lead in conducting searches. This has created some serious problems. For one thing, the Afghan troops are less forceful in conducting searches, and can often be dissuaded from searching rooms or buildings if the locals protest sufficiently. While American troops carry bolt cutters to take of locked rooms the owner is not willing to open, the Afghan troops will often just back off.
The Afghan security forces are also subject to bribes or intimidation. The Taliban or drug gangs will try to reach out to army or police commanders to bribe them to slack off during certain searches. For the police, who live in the area, the Taliban can often get the same result by threatening retaliation if a search is too successful. American troops often can detect when they are working with troops or police who have been compromised, but there's little that can be done.