TOC Levels Appear in reverse order.

Actually, you did a great job, I just forgot a step! My apologies. But based on what I can see, I think I was correct. You have a whole bunch of unthreaded frames. I created a rough draft of your layout below.

As the clip begins, I'm using threaded frames with the red headings. When I click a frame, you can see the blue lines that connect the frames, and changing one impacts the others. It looks essentially like your layout but because I'm using threaded frames, InDesign can see the exact order of the paragraphs and it copy them in the right order for the table of contents.

Midway through I break the frames (and change the heads to blue so that you can see the transition), and then I'm showing you that the frames are unthreaded. That's what causing the issue you are showing us. Sometimes you can cut and paste frames to get InDesign to see them in a correct order, and other times we can shift a frame left and other times, no matter what we do it doesn't work. Threaded frames always work. 

My suggestion is that you put the main content into threaded frames, and then InDesign will be able to straighten out the TOC. Don't worry about the content that isn't in the TOC—just focus on paragraphs I recreated. 

https://helpx.adobe.com/indesign/using/threading-text.html

~Barb

Can you please share a screen shot page page 2 or 3 (ideally both) with View > Extras > Show frame edges enabled, View > Extras > Show text threads visible?

Hi @crinderk87:

I'm guessing you're working with a unthreaded frames and InDesign is unclear about the frame order, but that screenshot will confirm it. We can also tell you how to thread them once we see what you're working with.

Please use the insert photos button on your reply instead of the attachment command. It's easier for us to see images inline rather than have to open up each file individually.

~Barb