Hi indy, welcome to the forum, and I'm glad that you are enjoying using MoI!

You can get that kind of behavior with Boolean Union when the objects that you are working on are open surfaces instead of all closed solids.

The booleans are oriented more towards working on solids - it makes it easier for the booleans to understand which pieces to discard and which pieces to keep when there are all closed volumes involved.

When there are not closed volumes involved, that "which piece to keep" logic becomes more ambiguous. When that happens you can be better off using Edit/Trim to cut pieces with one another, then that lets you more manually decide which pieces to discard, and then use Edit/Join to join the pieces together.

In your case here, your small piece is a solid, but the large piece seems to have had some faces deleted from it, making it a non-solid:





Also something similar on the other side as well it seems.

If you can finish that piece off to be a fully completed solid, then you should see that boolean union will behave more like you expected.

Otherwise, let me know if you would like to see some steps on how to use Trim + Join to bring those pieces together without doing a boolean.

- Michael