Tragically, Text wrap has always affected left side/first line indents within InDesign. More specifically, the text wraps affects the indents because your set indents don't change ...
Take a paragraph with a quarter-inch (.25 in) left-side indent and a negative quarter-inch (-.25 in) hanging indent. Those measurements are taken from the left side of the text frame. Now place a rectangular graphic on the left edge of the text frame and give it a half-inch (.5 in) text wrap.
This pushes any and all text a half-inch to the right of the graphic, which results in the bullet and second line of the paragraph aligned, and a default half-inch tab pushing the first letter of the first line further to the right. Your paragraph settings are what you set, but because the text wrap pushes your type past the margins you set, typesetting will be aligned by InDesign's default half-inch tabs from where your text wrap ends. That means everything lines up starting a half-inch in from the left edge of the text frame (the text wrap boundary), then left-align tabs set every half inch to the right side of the text frame.
The work-around is to:
- Zoom out to where you can see all the way across the text frame. Highlight the offending lines/paragraphs messed up by the text wrap.
- Use the keyboard shortcut Cmd/Ctrl+Shift+T (depending on whether you're using a Mac- or Windows-based version of InDesign) to open the Tab Ruler. Since you zoomed out to see the entire width of the text frame, by default it will line up perfectly with the text frame.
- Place your cursor on the bottom right-angled triangle at left. Hold the mouse button down and move it to the right until it lines up a quarter-inch past the edge of the text wrap. You'll notice that a vertical line moves with your cursor to show where the tab is aligned as you move. By grabbing the bottom right-angled triangle, it'll automatically move the top one, which is for the first-line indent, along for the ride.
- When you get it in the right place, release the mouse button and admire your handiwork.
This work-around should get your text alignment where you want it to be.