Paragraph Style Problem

Your paragraph style is set up as left-justified ().

This means that the last line of your paragraph will be aligned to left.

Since you have now plenty of single-line paragraph, they just align to left instead of justifying.

And I guess the unwanted left indents are just regular spaces...

Manually breaking sentences is a bad idea anyway. And you will never be able to keep hyphenation that way.

This was the theoretic explanation.

Now question is, how can you keep a flowing justified text while inserting lines in between?

That's quite tricky and you should probably give more details of the expected result.

But here's an example of a possible layout:

A text frame with your justified text.

And, on top of it, a bunch of threaded frames with text wrapping ON.