In the latest beta (2014.04.03 16:20) there are updates to the line
numbering system that break its function in columns. (In the past it didn't
work at all in many situations, not it works but in a buggy way).

In the example below, the line numbering passes over everything twice
resulting in two overlapping numbers for each line.

\starttext

\startlinenumbering
  \startcolumns
  \input{knuth}
  \stopcolumns
\stoplinenumbering

\stoptext