Minimal working example:
\version "2.18.2" \markup{"Grace note beams and slash cover ledger lines:"} { \clef bass \grace{ e,,32 f,, e,, f,, } a,,2 \slashedGrace{e,,8} a,,2 }
More info:
\markup{"Perhaps better would be:"} { \clef bass \once \override Beam.positions = #'(-0.5 . -0.5) \grace{ e,,32 f,, e,, f,, } a,,2 \once \override Stem.length = #11 \slashedGrace{e,,8} a,,2 } \markup{"Note that regular notes do not show this problem:"} { \time 5/4 \clef bass e,,32 f,, e,, f,, a,,2 e,,8 a,,2 }
More discussion here:
http://lists.gnu.org/archive/html/bug-lilypond/2016-12/msg00050.html