Please post a screen capture of the pages panel. Use the camera icon on the web page to embed it in a post like this:
In facing pages doduments, unless you disable page shuffling, even numbered pages are always on the left side of the spine, and odd pages on the right, which is waht readers expect to see (in versions that work with left-to-right text).
1) to avoid the numbering confusion, you need to change the numbering style on one of the sections. Front matter is often numbered using small Roman Numerals.
2) as noted before, even numbered pages are on the left, odd on the right. To restore order to you doc either change the starting number of the second section to an odd number, add a blank page at the start of the section and make it page 2, or select the spreads, then turn off page shuffling from the flyout menu.
3) the icon means there is transparency on the spread. If the pages are reshuffled to the correct order it will appear to the right of the entire spread. It's not something you can get rid of without eliminating the transparency, which could be an image with transparency, a drop shadow or other effect, or reduced opacity of an object tha you created.