When I go directly to a user's profile and see all their posts, sometimes one of their posts isn't in my timeline where it should be. I follow less than 100 users on Bluesky, but I guess this explains why I occasionally don't see a user's post in my timeline.

Lossy indeed.

If another user you follow reposted or replied to a post, it can affect its order in your following feed. You shouldn't be seeing any loss as described in the article from following only 100 users.

Are you using an app, website, or combination?

Various clients (I’m writing one) interpret the timeline differently, as a feed that shows literally everything includes could things that most people would find undesirable or irrelevant. (replies to strangers, replies to replies to replies, etc)