It's very difficult to reproduce this visually without the code you've used to trigger it. It looks like maybe you're using inputGroup--joined though which isn't expected to work here. That's designed to join two input elements (two basic form elements essentially, plus a few other specific use cases.
Certainly, one difficulty with a number box is that it itself is an input group so trying to join that to other input groups is not going to produce great results. Especially when it's trying to make a child within an input group (the - button) join onto a parent's sibling element (the select field).
I suspect you would be able to style this if you wanted, though it would be a bit hacky so it's just really not something we're trying to do here. Ultimately, all I can suggest is actually not joining them, which looks reasonable to me: