Converting a CIF file to a .com or .gjf file
In general, OpenBabel may convert some of the information of a .cif into a Gaussian .gjf.  If your are fine with using the CLI, the command would follow the syntax pattern of
obabel -icif input.cif -ogjf -O output.gjf
The parameters -icif and -ogjf hereby instruct OpenBabel about the expected input / output format of the files, while -O actually triggers the program to write the output into a permanent record.  Further information may be obtained here.
Depending on the computation intended, the crosses Mercury displays may be very valuable information.  It is Mercury's way to tell the user that the structure is disordered, i.e. there is more than one orientation of a molecule in the unit cell.  For example, that a conformational flexible $\ce{-CH3}$ or $\ce{-CF3}$ group has been refined into more than one position (think staggered / eclipsed conformation of butane, there are more than one energetic minima, and one is the absolute one.)  But this orientational disorder may extend over larger portions and complete molecules, too (e.g., small solvent molecules).  It would be better if you could display more of the structure, and tell a bit in addition about the intended computation.
Do you know to read a .cif file about site occupancy factors?  E.g., for molecules with an up / down or ($\uparrow$ / $\downarrow$) orientational disorder and only two realizations, these often are refined to add up to $p(\uparrow{}) + p(\downarrow) = 1.00$.