In some locations redstone components do not behave correctly. Updating the redstone by placing blocks next to it does nothing. It only happens in select locations so I can't give steps to perfectly re-create this. In the attached image I would expect the torches to turn off.
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That very well could have been the issue. The issue seems to have resolved itself without any special action. Just a server restart or two and it seems fine now.
If you have access to the world save file, please check whether MC-158219 describes your issue.