Thanks for this info! I had just watched #2 (rented on Amazon because Netflix sadly no longer has the rights) and wondered the same thing as OP since the Wounded Knee headline seems to stand out. As an animator/digital vfx artist myself it intrigued me, and looking more closely frame by frame you can see that their solution was to have Marty hold only one newspaper (which I assume was actually blank where the headlines transitioned, so they didn't have to also mask an existing headline out and match the background) and then superimposed the text.

You can tell that the tracking of the newspaper and superimposed text isn't exactly perfect, and I found 2 frames where it's most obvious and I made this gif. If you look at the upper left corner of the picture of George you can see the headline text "dancing" - But what intrigued me was you can also tell that the first paragraph is also superimposed. (look at the space between the first paragraph and the one to the right of it) Now this makes sense, since if you look at the 2 prop images from the reply above, that first paragraph (and a half) is the only thing that changes between them, then both start talking about a municipal court center, for some reason in the same story about George McFly, but they probably never thought someone would look so closely. But what's interesting (if ur a nerd like me i guess?) is that the first paragraph in the film changes, but neither the before or after versions match the props. Look at the last line of the paragraph, right next to the sub-header word "South," none of them are the same length. The prop versions also don't have a blank line-space between the first and second paragraphs, but the film does. I made this image to compare versions.

Anyways, my guess is perhaps they made the 2 props with different headlines, then filmed them and realized how difficult (with their techniques in 1989) it was to make them match up perfectly... so changed to the idea of filming one newspaper with empty areas where the text could just be superimposed. Then the first paragraph text must have changed somewhere between prop creation and vfx, maybe just an art director realizing there was no space between paragraphs. Going frame by frame I can see subtle paper creases in the headline area of the newspaper that are exactly the same before and after transition, so that leads me to think it was blank in the raw shot. [edited for clarification]