That is odd: I have one theory as to how this might happen. See below.
FYI, for anyone following along, this is PR 2020 or before with the "old" caption workflow. PR 2021 introduced a new method. There may be other issues, so I am not recommending that you change.
Note that in your second screenshot, even though you show a different caption in the Program Monitor that is lower on the screen, you have the save caption selected and showing in the Caption Panel. So we are not seeing the caption settings for that caption. But I can't see that it matters!
The "lower" caption is at the very bottom of the frame. It is not possible to get a caption that low without applying the Effect Controls position to move the whole track down. Then to get the captions that show higher up, you can add a "return" at the end of the caption text. When I do this, because I have a background box, I can see there is an extra line. If I don't have a background box (as you do not), then I don't see that there is an extra line.
To test that theory, edit one of the captions that is higher, and see if you can delete an extra line.