TLDR: Ensure both objects are "Union" through Boolean before making a difference.
I have a problem with Booleans whenever I use difference with 2 different objects. I will elaborate my problem.
Steps:
1. have 2 cubes (one smaller than the other), both of which are intersecting one another
2. select the bigger cube then the smaller cube, then head to Mesh > Booleans > Difference (I'm using with default settings). and you'll be presented with this:
3. Combine (Mesh > Combine) an object that I want to make a hole with the cube object. In this case, I have a cylinder and 2 spheres to create a capsule object
4. Place it in the cube so that I have another hole and do the same (Mesh > Booleans > Difference). If you do so, you'll either have the original cube disappear together with the capsule object. I tried extracting the face, like this youtube video suggested, that I want to add a hole but I got a wonky face.
if you happen to have this problem, here's just ensure both objects' individual parts are "Union"-ed with Boolean (Mesh > Boolean > Union) and not Mesh > Combine.
I'm not entirely sure this is an intentional feature. Anyways, hope this helps.