You don’t have to scroll all the way down to the bottom to mark a topic as read; just viewing it (any page) should do it.

Certain data is cached to improve performance, such as the header content (which includes the bubble). When you view a topic, that clears the header cache, but occasionally the refreshed header will load before the topic is marked as read in the database, which means the unread bubble is cached again. I’ve seen it get out of sync like this occasionally and will take a look at fixing it. Logging out and back in should clear it.