Further experimentation suggests that the problem is in the interaction between footnotes and margin placement. Endnotes work fine.

\defineconstructionalternative
  [mylabel]
  [renderingsetup=constructionrenderings:mylabel,
   width=]

\startsetups[constructionrenderings:mylabel]
  \dontleavehmode
  \inright{\flushconstructionheadbox}
\stopsetups

\defineenumeration
  [one]
  [alternative=mylabel,
   display=no,
   before=,
   after=]

\definenote
  [endnote]
\setupnotation
  [endnote]
   [way=bytext,
    location=none,
    conversion=numbers]

\starttext

    \startchapter[title=bar]

        this works \startone[reference=aa]\input jojomayer \stopone
        \quotation{\startone[reference=bb]\input ward \stopone}

        this fails\footnote{\startone[reference=cc]\input jojomayer \stopone
        \quotation{\startone[reference=dd]\input ward \stopone}}

        while this works\endnote{\startone[reference=ee]\input jojomayer \stopone
        \quotation{\startone[reference=ff]\input ward \stopone}}

        whatever \in{one}[aa] whatever \in{one}[bb]

        whatever \in{one}[cc] whatever \in{one}[dd]

        whatever \in{one}[ee] whatever \in{one}[ff]

    \stopchapter

    \startchapter[title=notes]

        \placenotes[endnote]

    \stopchapter

\stoptext

--
Rik