I wanted to shed some light on this.
I have the same issue on my site and have a way to reproduce it.
The only way I can reproduce this 100% of the time is to disable javascript. And on the /checkout page there will be a “Update totals” (inside a <noscript> tag)
Once you click on this it will reload the page and the discounts will not be applied. (Yet it will say X% discount has been applied)
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I’m not sure how to reliably reproduce it otherwise, but I have seen orders here and there show up with this issue. (And I know they don’t have javascript disabled)
I can’t seem to recreate the update totals logic with javascript enabled, so I’m not sure why or when its occurring.
Hope that helps,