This runs without error and I think gives the intended layout, although I
can not read the text, sorry.
\documentclass{article}
\usepackage{libertine,media9,polyglossia}
\setdefaultlanguage[variant=british]{english}
\setotherlanguage[]{hebrew}
\begin{document}
\marginpar{\includemedia[
label=song49,
activate=pagevisible,
deactivate=pageinvisible,
noplaybutton,
flashvars={source=http://www.kfeuerherm.ca/IntHeb/BBE.mp3&hidebar=true},
transparent
]{\makebox[1cm]{x}}{APlayer.swf}\mediabutton[mediacommand=song49:playPause,tooltip={Play/Pause}]{(P)}\mediabutton[mediacommand=song49:play[(0.0)],tooltip={Reset}]{(R)}}
\begin{hebrew}
\textenglish{\mediabutton[
mediacommand=song49:play[(0.65)],
mediacommand=song49:pause[(1.45)],
overface=ONE
]{\texthebrew{בראשׁית}}}
\textenglish{\mediabutton[
mediacommand=song49:play[(1.8)],
mediacommand=song49:pause[(2.45)],
overface=TWO
]{\texthebrew{ברא}}}
\textenglish{\mediabutton[
mediacommand=song49:play[(2.8)],
mediacommand=song49:pause[(3.8)],
overface=THREE
]{\texthebrew{אלהים}}}
\end{hebrew}
\end{document}
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