water in closed system is pretty dirty and rusty despite o2 barrier PEX. Is this normal?

DIYer here. I designed and retrofitted this heating system in my home 2 years ago when I was starting my basement remodel. This is the 2nd season of heating. I'm in a cooler climate out west, so can use heat anytime from October-May typically. The system initially went live with 2 zones - radiant floor zone with 7 circuits for my main floor, and a higher temp panel radiator zone for my top floor. Last summer I added 2 more radiant floor zones (2 circuits each) in my basement. There is probably about 35 gallons of water in the system. The system uses o2 barrier PEX throughout (mostly PEX-b, except for the basement which is PEX-AL-PEX). The boiler is a Noritz combi boiler that also does my DHW.

Last summer when I added the basement zones I noticed that the water was really dirty so I decided to put in a Adey magnetic filter. At that same time I flushed the system with clean water (I didn't put any cleaner in prior to flushing). I recently checked the magnetic filter and again found the water to be really dirty - there were a few tablespoons of metal "mud" that the filter had caught. Is this just normal operation? Is it the result of adding the new zones?

My plan is to put in a cleaner like MC3+ for a few weeks prior to flushing with new water. I'm guessing I also need to add an inhibitor. The water I am putting into the system is my domestic well water post whole-home sediment filter and water softener. Also note, that there was some air in the system as a result of a leak I had to repair after puncturing the PEX during flooring install. That air has since been bled out of my radiators on the top floor. I had a plumber recommend putting in glycol, but general sentiment i've read on here is that's a bad idea.