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I think you're using Mastodon's advanced mode with its pinned tags.
That's a totally separate system from hashtag following.
If you've been away a long while, it may be that you are seeing the advanced mode by default. Multicolumn was replaced with a simpler single column interface as default, with multicolumn made an optional mode.
You can switch modes by going to Preferences > Enable advanced web interface, tick/untick to activate/deactivate, click Save Changes
@feditips Yes, I'm using the advanced mode with multiple columns. I very much prefer the multi instead of single (on desktop). It's also the only way I've found so far that groups multiple hashtags together in a single column instead of switching between one for each. Switching would be a pain for hashtags such as #3dprint, #3dprinting, and #3dprinted which all give different results for the exact same topic.
If you follow hashtags in single column, they are all grouped into your Home timeline.
Pinned tags and followed tags work totally separately, as pinned were there a long time before following was introduced.