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in OJS 2.3.1 there was in Setup 3.1 the option to "Allow authors to separately provide a formatted list of references (citations) as part of their submission."
Now, in a 220.127.116.11 I can't find it and, for each published article in the landing page, I see a title for a "References" also if the list is blank.
Why did you choose to upload separated refereces as mandatory? I think there is a compatibility problem with previous issues.
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I've replicated the issue regarding "References" always displaying, and have submitted a report here: http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=6119
. Please CC yourself to that report for future updates. Also, the previous option in Setup Step 3.1 has now been moved entirely to Setup Step 3.7 -- the option to upload references separately now only appears to Authors if the Citation Markup Assistant has been enabled. Editors can still manage references the old way -- via the submission's Metadata page -- so there should be no incompatibility with older versions of OJS. This was our intent, but I can understand how it could be confusing.
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