Lilypond appears to group notes in different voices together as a chord

[A Jakovljevic]

Adjusting the allocation of the notes between the voices to match what is
in your source (apologies for using the abbreviated syntax here, for a one
measure example it should be clear enough) should do the trick, no?

\relative c' {
<< { s2 d'4( e) } \\ { f,4~ <a f>~ <a f>~ <d a f> } >>
}

Cheers,

Aleksa