I could reproduce this occasionally occuring unexpected output in following MWE.

Seems linked to calt=yes feature being set and ordn=yes being set and letter ‘f’ (some other letters such as ‘b’ work fine).

Thanks as always for help.

\definefontfeature[noteref][mode=node, ordn=yes]

\definefontfeature[default][default][calt=yes] % works if calt is not set

\definefontfamily[mainfont][serif][EBGaramond]

\setupbodyfont[mainfont, 9pt]

\define[1]\Sup{{\feature[+][noteref]#1}}

\starttext

\dontleavehmode e \Sup{f}*word % f is not superscript if calt is set

\dontleavehmode e \Sup{b}*word

\stoptext