Hard to tell from the pics, but those cakes look dry and they definitely need more FAE. Aerial myc (the stuff reaching for the sky) is a dead giveaway.

As dry as they look, you may want to double check your humidity.

Dryness can cause bruising, so that might be what's going on there. Mist and fan - mist and fan. I know you're shooting for as much automation as possible here, but a little TLC goes a long way with shrooms (and A LOT of TLC goes a LONGER way, lol).

Evaporation of water from the surface of the substrate is also a big - if not the biggest factor in pinning.

I'd bet a bong and a blintz that if you start misting and fanning 3-4 times a day your plan will right itself.

As for the water - I can only speak to my experience, but I always just fresh cold tap water (from a well) for my dunk and the post dunk rinse and haven't had an issue with that as a vector of contamination. Fully colonized cakes are actually more contam resistant that a lot of folks realize.