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