At the bottom of the tools panel there are fill/stroke icons:
Whichever one appears 'on top' is the one currently targeted. You can change which one is targeted by clicking on them (or performing other actions, such as adjusting stroke alignment as you discovered above).
A bug was introduced in the most recent Illustrator update -- as such, whichever appearance (stroke or fill) is currently targeted is the one controlled by the colour sliders in the stroke and fill controls in the Control bar and Properties panel. The Illustrator team are aware of the bug and intend a fix in an upcoming release.
Bugs are unfortunately an expected part of using the newest major releases of software. I'm happy for you that this is your first such experience.
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