Dear @Lukas-jd,

To remove the negative frequency you can try two procedures.

Re-optimize the initial structure with a larger tolerance. You can make use of the EXTERNAL keyword using the f34 of the previous optimized structure. 
For example:

EXTERNAL
OPTGEOM
FULLOPTG
TOLDEG
0.00010
TOLDEX
0.0004
TOLDEE
11

Run the SCAN-MODE to eliminate the negative frequency (see page 194 of Crysatl User's manual). To run the “scanmode” calculation: select the mode you want to eliminate; make an EXTERNAL, the f34 is the same used before; select the initial, final, and the step for the scan; run the calculation

Example for the input:

EXTERNAL
FREQCALC
SCANMODE
1 -10 10 0.4 (number of the mode to eliminate, first step, last step, step displacement)
2                    (sequence number of the modes selected)
END
END
basis-set and etc

after finishing the scanmode calculation, open each SCAN_ file and plot a graphical of mode x energy (see example on user's manual). vi. the minimal point should be your structure with minimal energy and no negative frequencies; vii. run an optimization making an EXTERNAL from the SCAN_file (that is the f34) of the minimal energy found before; viii. after, run the FREQCALC again.

Now, it should not appear negative frequency.