Ashley, I believe this is how PDF format actually stores text inside. When it comes to kerned pairs (ruled by Auto or Optical or just a manual kerning parameter in the Character panel), the lines of text get split and nudges to respect the kerned distance between chunks.

What Acrobat do to hide it is that it allows to select text continuously. It’s easy to verify if you put two separate lines next to each other, save a PDF, and try to select them in Acrobat — it will allow to continuously select them as if they were one line.

Another solution PDF uses to maintain the look is to convert kerning into tracking instead — this allows the lines to stay as a whole.
I do not know specifically when it prefers one method to another, and I will try to search info about that.

However, in the meantime we have to deal with these somehow.
There are four methods I know of:
1. Manual one — grab chunks one by one, cut them and paste as text into the main chunk. Boring and long.
2. Scripts: Join TextFrames by John Wundes, MergeText_AI by Justin Putney, other ones — they are all limited and slow, but free
3. VectorFirstAid plugin by Astute Graphics, the Combine Point Text Objects button specifically. The best one, the paid one — it’s a part of their superb plugin pack, provided by subscription. Requires to select broken characters first to get a proper result, as lines or whole paragraphs.
4. Recent new Retype feature. But it works only with outlined (or rasterized) type, works on per-word basis only, doesn’t support rotated text (unlike #3), and can’t promise the exact match — just because the original purpose of the tool is a different one.

But thanks for raising the problem.
That’s why Illustrator is not a general PDF editor and isn’t supposed to be one. Remember, 'opening' a PDF is always 'importing' one, with the restrictions applied, unless you save this PDF with the compatibility option checked (which just writes a whole Ai-documet copy inside). That’s also why you get a ton of clip masks in places you never had them, extra objects, etc. PDF is not a native Ai format and will never be: Illustrator has some objects have to be expanded for Acrobat and other apps to view, and PDF can store objects Illustrator will never be able to display — like videos.