Maarten,
You have a typing mistake in the line creating the 3rd branch (dot instead of comma).
This line should be:
    muontree->Branch("EndVertex",&end_vertex,"Xvert2:Yvert2:Zvert2");
If you make this change, your program will work.
 muontree->Print() will produce:
root [7] muontree->Print()
************************************************************************************
*Tree    :muontree  : Data for all muons                                           *
*Entries :        0 : Total  Size =         0 bytes  File  Size =          0 bytes *
*        :          : Tree compression factor =   1.00                             *
************************************************************************************
*Branch  :Momentum  : Px:Py:Pz                                                     *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
*Branch  :Begin_Vertex : Xvert:Yvert:Zvert                                            *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
*Branch  :EndVertex : Xvert2:Yvert2:Zvert2                                         *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
*Branch  :Tracklength : Tracklength                                                  *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
*Branch  :P         : P                                                            *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
*Branch  :Pt        : Pt                                                           *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
*Branch  :Mother    : Mother/I                                                     *
*Entries :        0 : Total  Size =         0 bytes  File Size  =          0 bytes *
*Baskets :        0 : Basket Size =     32000 bytes  EvOffsetLen=          0       *
*        :          : Branch compression factor =   1.00                           *
*..................................................................................*
Rene Brun