You can put a box over a bees nest as there is still room for the bees to get out.

Chapter 316 Section 5

If two people close the door on a deer, but the door could have been closed by only one of them, it is only prohibited rabbinically.

Once the door is closed, you can lock it.

Chapter 316 Section 6

If a person stood in a doorway to block the entry which is prohibited, another person is allowed to stand behind him and even if the first person leaves he is still allowed to be there.