Crates.io recently switched from counting downloads via requests to the application to counting downloads by parsing CDN logs. Here's a zulip thread about it; I think a blog post is coming soon. https://rust-lang.zulipchat.com/#narrow/stream/318791-t-crates-io/topic/download.20counting.20via.20CDN.20logs
There are some tools/mirrors that were hitting the CDN directly: those downloads weren't being counted before and now they are.