When changing out something on a water system on a well it's not uncommon for a lot of accumulated minerals to let loose. The minerals have been attaching themselves to your plumbing for years. When you disturb them, they break loose and head downstream. If there is a reduction in pipe size along the way, these chunks can get lodged there and restrict flow. Same with the faucet strainers and the faucets themselves.
Is this problem at all fixtures or just some of them?