Footnote Adds Extra Space Above Span Columns in InDesign

I could not, at first, quite figure out how you set this layout up. It's a bit wonky and that's what's causing the weird behavior. I can pass back a fixed INDD but it should be:

• Set up as a 2-column frame with a gutter (it's a 1-column frame).
• Bullet style should be single-column (you have them splitting columns).
• Heading and body text should be set to span columns (they're single column).
• Body text should have some space defined below span (it has zero).
• Footnote should have its own style, also set to span columns (it uses the base style).

Other than some formatting details, you have two problems here: you used/based everything on [Basic Paragraph], which is a general no-no; all paragraphs in a doc should originate from "No Paragraph Style" or a previously defined style. Never use the [Basic] or [Default] styles of any kind, for anything.

And, the major issue, you set this up to have the bullet style split columns, which is a wonky feature I've never found stable. It's better to define your multiple columns at the text frame level and then selectively span them, rather than have a style force a virtual column split. Maybe there is some way to fix it around a split, but flipping the model cured the weird spacing problem. (I suspect split + balance columns is fighting over who gets to control things, as well.)

The footnote no longer has any unintended effect on the layout; again, it might have been confusing the balance-these-fake-columns process.

That help?