Dirty water in 3-Piece shower/tub seams

I have a shower/tub 3-piece system that lately, when scrubbing the seams with a toothbrush and later rinsing it, a smelly black colored water will come out. I immediately grew concerned because I don’t want any mold behind my walls and was wondering if something is wrong.

I did a bit of research and found almost the exact model I have http://oasisbath.com/tubs-showers/product/470/. I also later found the installation manual and realized that these systems have a flange that would keep water from getting behind the walls but they need to be sealed as shown here. Unfortunately I can’t see inside the seam and based on the photo, I don’t think its meant to keep water out anyways since a small gap and now you are trapping water back there.

I was wondering if there was something I could do to prevent this or its just one downfall of these systems? Should I be concerned with mold even though I am pretty sure its just mildew or something similar? By the way, the bathroom is only 4 years old.

Thank you.