Ive made a mod that features 100 mens action magazines from the 50's and 60's and placed them throughout the fallout world. How do I solve the problem of the player getting penalized for stealing when picking one up in an NPC house or territory? Do I have to make a quest?

You can set the ownership of the items to player. Rightclick the item in Cell View window and choose Edit. Click the Ownership tab and choose Player in the NPC dropdown. That should solve it.

Items without a specified owner inherit the ownership of the cell or container in which they're placed. That's why it's necessary to do what Zumbs said.

If such items are placed in an unowned cell, there is no ownership to inherit, so they're free to take.

Thanks for the replys, you were right and I got it sorted out.