I assumed those were drain holes. If you ever flood out the floor, by leaving a window open in the rain or having the AC drain clog, or a msasive spill, you can pull those plugs to help let water out. The plug in the picture was pushed in somehow, fish it out, then press it back into place from underneath. The Vibe I have now I bought used, it was missing one of those plugs. I RTV'd a can lid over the hole to keep road spray out.
if there's bare metal then maybe it got scraped on some road hazard, maybe touch it up with some naval jelly and throw a quick spray of primer over it
The connector/wires are for the oxygen sensor, I've seen several, your's looks normal to me, no worries