Issue:
When using multiple boolean modifiers, the objects (other), don't subtract properly from the object (self), causing issues with the object (self) mesh.

Possible Causes:
The issue seems to occur when the added objects (other) intersect along another objects (other) face.

Temporary Solution:
When applying the boolean modifier, create a new mesh, with the linked properties from the old object (self), to the new object (self), allowing the user to continue adding other objects (other) to use with the boolean.
This should be a temporary, automatic solution.

User Workaround:
Scale each individual object (other) by one unit, the avoid this issue, just make sure the objects (other) do not intersect along the object (other) wireframe.