Leaving the pot out overnight has never been a problem for me, as long as I keep the lid on it. A less-than-sterile dishtowel would definitely be enough to cause some contamination though. I use disposable coffee filters to cover the jar, as they are cheap and I don't have to worry about whether they've been washed well enough.
You shouldn't put the glass lid over your towel/filter because the kombucha needs to be able to get air. That's why you use a porous cover. I don't think this would cause mold though.