They are fine.. brown with no slime or stink just means they are stained from fertilizer or substrate.
whether in the pot or not, sitting in the pool of water is the cause of risk. inside the fabric or not at bottom makes no difference.. in fact better without light.
anyay, a pot shouldn't sit in it's runoff. that's the danger here - overly wet, anaerobic conditions = bad bacteria potential. the roots that escape the pot should air prune themselves, but swill of runoff water is clearly preventing that.
you could prune them off (and without doing anything about cause will have to do so repeatedly until end), but you also want to use some sort of riser/grill for your pot. A big benefit of fabric pots that the roots will air prune themselves instead of wrapping around over and over (cause of rootbound). if it sits in runoff that may be reduce at bottom. depends on how long it stays moist and how long it dries out between irrigations.