Thanks for the detailed report. To summarize, I see two different issues here:

1. A visual editor edit generated wikitext like this, which is incorrect – the reference theodore is defined twice with different contents:

|-
|{{convert|142|mi|50|chain}}
|[[Kaloola railway station|Kaloola]]
|{{Coord|-24.8487|150.0624|type:railwaystation_region:AU-QLD|name=Kaloola railway station (former)}}
|{{convert|531|ft}}
|<ref name="railwaystations" /><ref name="theodore">{{Cite web|date=1972|title=Theodore|url=https://gisservices.information.qld.gov.au/arcgis/rest/directories/historicalscans/cad_scans/cad-map-100000-8948-theodore-admin-bdy-1972.jpg|url-status=live|access-date=18 January 2022|publisher=[[Queensland Government]]|type=Map}}</ref>
|-
|{{convert|146|mi|72|chain}}
|[[Goolara railway station|Goolara]]
|
|{{convert|461|ft}}
|<ref name="theodore" />
|-
|{{convert|149|mi|72|chain}}
|[[Theodore railway station, Queensland|Theodore]]
|{{coord|-24.9491|150.0820|tyoe:railwaystation_region:AU-QLD|name=Theodore railway station}}
|{{convert|461|ft}}
|<ref name="theodore">{{Cite web|date=1972|title=8948 Theodore|url=https://gisservices.information.qld.gov.au/arcgis/rest/directories/historicalscans/cad_scans/cad-map-100000-8948-theodore-admin-bdy-1972.jpg|url-status=live|publisher=[[Queensland Government]]|type=Map}}</ref>
|}

2. When you load that page in the visual editor again, the second definition of the reference behaves strangely:

Change 755739 had a related patch set uploaded (by Bartosz Dziewoński; author: Esanders):

[mediawiki/extensions/Cite@master] ve-cite: Handle ref nodes with mw:Error RDFa

https://gerrit.wikimedia.org/r/755739

(this patch fixes issue #2)

Change 755739 merged by jenkins-bot:

[mediawiki/extensions/Cite@master] ve-cite: Handle ref nodes with mw:Error RDFa

https://gerrit.wikimedia.org/r/755739

If you are looking at the current version of my sandbox5, then it's been fixed manually (or so I thought, I obviously missed the 2nd theodore reference). I had to as this is actual content I am working on so I had to fix it; it wasn't just some kind of test. If you look at [https://en.wikipedia.org/w/index.php?title=User:Kerry_Raymond/sandbox5&oldid=1066408215 this version], you will see dozens of repeated citations instead of extensive re-use of a number of them

@Kerry_Raymond Thanks for pointing it out, indeed I was looking at the latest version. I followed the link you gave: [https://en.wikipedia.org/w/index.php?title=User:Kerry_Raymond/sandbox5&diff=prev&oldid=1066407160] and I didn't notice that Phabricator includes the ] at the end in the link URL, which causes MediaWiki to show the latest version instead of the one you meant to link to.

I was also confused by the phrase "not reusing" – I understood that to mean that you copied the reference in a scenario like this:

…and ended up with this:

…instead of this:

…but of course that's not what you meant, and not what happened. I'll change the task title to clarify.

Now that I know what I'm doing, I can easily reproduce this: https://en.wikipedia.beta.wmflabs.org/wiki/T299378

Further notes:

• The table isn't required to trigger this, refereces in plain text are affected too
• Only references inserted in the same edit trigger the issue – copy-pasting references that were already on the page works fine
• Using Cite → Re-use instead of copy-pasting also triggers the issue

That's interesting. My impression was that Cite Reuse seemed to be working ok. But I had not noticed that "Only references inserted in the same edit trigger the issue", so it may be that I was only observing Cite Reuse in the context of reusing a reference being created in a previous edit.

I think this bug is fairly recent (within the last week or so). I had noticed on my watchlist that others were editing articles I had worked on and were replacing duplicate citations with citation reuse. The first few times I saw this, I just thought, "silly me, I must have added that citation twice". But when it happened a few more times and I started thinking "how on earth can I be doing it so much, and just in the past few days, what I am I doing differently to my usual editing style?". It was only when I saw it happen on a massive scale in my sandbox5 which I had just finished editing and had done so in a very formulaic way that I noticed that the duplicate citations had the same VE-generated names, e.g. <ref name=":01"> and I was not re-entering the citation multiple times as VE would have named them differently even if the content was the same. That was the "there's a bug" moment.

Caused by rECIT1a2ae0682fac: ve-cite: Use proper method for comparing linear data (attempt 2) (November 2021).

Change 757553 had a related patch set uploaded (by Esanders; author: Esanders):

[mediawiki/extensions/Cite@master] ve-cite: Ensure references are always unique by generating originalDomElementsHash

https://gerrit.wikimedia.org/r/757553

Change 757553 merged by jenkins-bot:

[mediawiki/extensions/Cite@master] ve-cite: Ensure references are always unique by generating originalDomElementsHash

https://gerrit.wikimedia.org/r/757553

I have checked to confirm that Visual Editor does not duplicate content when reusing/copy-pasting newly added citations.

See https://photos.app.goo.gl/y6qk9zW4f3S74jvU7 to confirm that it acts as expected.