Why are my audiobook chapters out of order?
It's sort of the same solution to "Songs show up as individual albums in iOS Music app."

Make sure the files have the correct tags for album, artist, track, and title.

Then in iTunes:

1) Upload the first track to Music.

2) Upload the rest of the tracks to Music. (Or you can upload all the tracks including the first one -- iTunes will ignore the duplicate first track.)

3) Select all the tracks in iTunes, right click, then select Get Info > Options > media kind > Audiobook, and click OK.

iBooks should list the audiobook in order now.

The key is that the first track of the audiobook must be uploaded first.

P.S. You can also upload multiple audiobooks by doing steps 1 and 2 on the first audiobook, then repeat for the other books. And then select all and do step 3.

Or do step 1 on each audiobook, then do step 2 on all the audiobooks together in one go, then select all and do step 3.