We just started this new glitch where replies to a post are shown as being from “System” user. (The post is attributed to the correct user, but the reply sometimes is not). I checked with the poster and he was not posting in anonymous mode.
We were running v3.1.0beta4 (which did not include any of these changes) up till 10am today, so the issue is probably in that tag.
I can give you a bit more info, this was during the upgrade process, but prior to the upgrade actually finishing. We have a deployment upgrade process that, in part, sets a global notice banner that the site will go down shortly and leverages the API, authenticating as the system user to do so. The job actually failed due to an out-of-date part of the build pipeline and left the banner up for ~10 hours before it was fixed and the upgrade finished. All of the comments that appear to be coming from the “system” user appear to have happened roughly around the time that this banner was set and up (yes, this seems quite odd). After the upgrade the problem doesn’t appear to have resurfaced. So, yes, the bug appeared to be surfaced while we were on v3.1.0.beta4.
Perusing through the code, the only thing I noticed involving users and notices is an after save hook on users that appears to be potentially clearing a global notice. So this could very well be a theme or plugin causing the issue, but either way my money is that it has something to do with the API request that was authenticating as the system user given the timing and the associated user.