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Treat the infected shrimp outside the main tank.

I would just treat the quarantine tank first and see if that is effective in the treatment. I have that malachite green and it will seriously stain everything it comes into contact with, so wear gloves and be very careful. If it works successfully then consider doing the main tank later if you are still seeing sick shrimp in it, but it may result in you having to redoing the tank once you have treated it.

This week I noticed that some of my yellow neos developed white patches on their gills. I quarantined them as soon as I saw something was off. As the week went on the patches got a red edge, and almost look like blood? Both sides of the shrimps are affected (slightly symmetrical), and the edges seem to be darkening. It doesn't seem like Rust disease because it's localized to the gill area, so I'm stumped on whether they just got unlucky with some water parameter changes, or if it's something serious? I've browsed the diseases topic and none of them seem to match. They're also eating/acting fairly normally in the quarantine tank. Would appreciate any advice! I've attached a photo below.