Was this resolved? Or, have you seen it re-occur?

A doubt.
Before submitting the API request in site.py:

if lastrev is not None:
            params['basetimestamp'] = lastrev.timestamp

The timestamp has been updated to the value of the other edit, so no edit conflict appeared.
Shouldn't basetimestamp be the timestamp of our current page instead the one of the latest revision?

The problem here is that we should timestamp (using touched timestamp when retrieving it) the text that we are going to modify and use that timestamp as basestamp in editpage.
The tricky part to me is to understand when the text that is going to be modified is loaded. First access? When page._text is first created?
Updating timestamp every time page._text is updated is not reliable, as a call to page.latest_revision updates page._text as well, and this might happen also after the bot has modified the intended text.

I did this hack:

oldRawVMText = vmPage.text
rev_id = vmPage.latest_revision_id

for reading and a sanity check before writing:

# sanity check
if vmPage.latest_revision.revid != rev_id:
    print('Revision ID changed')
    raise pywikibot.EditConflict
vmPage.put(newRawText,
           u"Bot: Abschnitt%s erledigt: %s" % (('', 'e')[bool(userOnVMpageFound-1)],
                                               editSummary + openSections +
                                               oldestHeadlineWithOpenStatus),
           False, minorEdit=True, force=True)

With this change, I think this should not happen any more:
https://gerrit.wikimedia.org/r/208574

@Xqt, if you keep your patch and you see a conflict also after pulling this change, please notify.

I've been working on a test case and it shows that there still seems to be a possibility for an EditConflict (or I misunderstood how it works): https://gerrit.wikimedia.org/r/215338

Strange. I tried on en.wikisource but I got an edit conflict.
Might be a wiki-specific setting?

>>> site.login()
Logging in to wikisource:en as MpaaBot
>>> page=pywikibot.Page(site, 'User:Mpaa/x')
>>> page.latest_revision
{'comment': u'test', 'text': u'[[Category:Male authors|test]]\n[[Category:1 births|sortkey]]\n\n{{test|test1}}\n{{test|test1}\n{{test|test1}}', 'revid': 5432692, 'anon': False, 'user': u'Mpaa', 'rollbacktoken': None, 'timestamp': Timestamp(2015, 5, 23, 15, 42, 13), 'minor': False}
>>> site.user()
u'MpaaBot'
>>> page.text = 'reset'

... In the browser I saved an edit as Mpaa ...
https://en.wikisource.org/w/index.php?title=User:Mpaa/x&diff=next&oldid=5432692

>>> page.save(summary='test again')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/squiddy/python/core/pywikibot/tools/__init__.py", line 1102, in wrapper
    return obj(*__args, **__kw)
  File "/home/squiddy/python/core/pywikibot/page.py", line 1061, in save
    cc=apply_cosmetic_changes, **kwargs)
  File "/home/squiddy/python/core/pywikibot/page.py", line 1085, in _save
    raise err
pywikibot.exceptions.EditConflict: Page [[en:User:Mpaa/x]] could not be saved due to an edit conflict

Hmm weird. It now works for me too and it raises the EditConflict exception. Of course it's unusable without two accounts working at the same time though.

This bug is still valid. The following occurred:

1. page has been written by a user [1]
2. bot reads that page (via preloading)
3. page has been changed by same user [2]
4. bot checks whether page has been changed and saves it [3] but it was the old text

[1] https://de.wikipedia.org/w/index.php?title=Wikipedia%3AAdminwiederwahl%2FHolmium&type=revision&diff=151344424&oldid=151254490
[2] https://de.wikipedia.org/w/index.php?title=Wikipedia:Adminwiederwahl/Holmium&diff=next&oldid=151344424
[3] https://de.wikipedia.org/w/index.php?title=Wikipedia:Adminwiederwahl/Holmium&diff=next&oldid=151431668

the code looks like

text = page.get()
restrictions = page.getRestrictions()
head = ''
text = head + text
old = page.get()
if text != old
pywikibot.showDiff(old, text)
page.put(text)

The second page.get() wasn't forced; it's unclear why it was reloading from live wiki.

Another sample to investigate into this matter:

>>> import pwb, pywikibot as py
>>> s = py.Site()
>>> p = py.Page(s, 'user:xqt/Test')
>>> t = p.text
>>> p.latest_revision_id
151438066

# now change the page online!

>>> r = p.getRestrictions()
>>> tt = p.text
>>> p.latest_revision_id
151438784
>>> t == tt
False

Change 270598 had a related patch set uploaded (by Xqt):
Workarround for overwrite conflict.

https://gerrit.wikimedia.org/r/270598

Change 270598 merged by Xqt:
Workarround for overwrite conflict.

https://gerrit.wikimedia.org/r/270598

See also https://de.wikipedia.org/w/index.php?diff=169721937

Maybe an upstream problem?

There is another case reported with https://en.wikipedia.org/w/index.php?title=User_talk:Xqt&oldid=1017350521#Bot_bug?

One bot task of Redirect.py edited the page correctly: https://en.wikipedia.org/w/index.php?title=User:1234qwer1234qwer4/Xqbot_bug&diff=prev&oldid=1017183095 but the second task made this malformed change at the same time.

Both bot tasks have the same user and IP.

Another strange edit was found here but no second editor was involved. All Tests worked as expected later: https://fa.wikipedia.org/w/index.php?title=%D9%88%DB%8C%DA%A9%DB%8C%E2%80%8C%D9%BE%D8%AF%DB%8C%D8%A7:%D8%B2%D8%A8%D8%A7%D9%86%E2%80%8C%D8%B4%D9%86%D8%A7%D8%B3%DB%8C_%D9%88_%D8%AA%D8%B1%D8%AC%D9%85%D9%87/%D8%A8%D8%A7%DB%8C%DA%AF%D8%A7%D9%86%DB%8C_%DB%B1&action=history
Probably an upstream problem?

Again: https://de.wikipedia.org/w/index.php?title=Benutzer_Diskussion:Basti_Kaspar&type=revision&diff=218356378&oldid=218356376&diffmode=source