What type of marker did you use? Is the marker supposed to be dominant or codominant? Do you have a pic of the gel?

There are a lot of possible explanations for an unexpected band on a gel. With more information we may be able to narrow the list down to a few likely candidates.

if this is a pcr assay and you expect this sample to be negative what does your water blank look like. If this also has amplified bands then you have pcr product contamination of one of your reagents so everything will look positive. Can we see a gel picture please?

Dear all, SSR marker produced a 243-bp fragment in negative control ‘Morocco’

SSRs are typically codominant, meaning that alleles can be distinguished based on their size (rather than based on presence or absence). What size is the fragment in your positive control?

Positive control showed a smeared pattern. For another gene, two dominant markers, BE518379 and Sr26#43, were used in combination. These markers produced a 207-bp band only in positive control, whereas a 303-bp band was observed in varieties and the negative control. 

First:

Are the smears high-weight or low weight?

Smears not caused by contamination (in the template, master mix, or gel lane) are generally due to nonspecific amplification. This might occur if you have poor quality or degraded template DNA or if your PCR conditions were such that they allowed the primers to bind to non-target sequences.

Is your template DNA for the positive control of high quality? Have you checked it by spectrophotometer?

Is the smear for the positive control similar to what you observe for the water blank control? Is your water clean and sterile?

What is the concentration of template DNA in your reaction? What is the concentration of each primer? Overloading template can cause nonspecific amplification.

Is it possible that the positive control reaction was subjected to different conditions than the other wells? I mean, could it have been in the corner of the block, not seated properly, etc.? Have you repeated these reactions with the same results? Have you tried running the positive control in a different well?

Second:

For dominant markers, I would recommend running them in separate reactions (and gel lanes) until you are certain they work well and you know what to expect.

Based on your description of the results from the two dominant markers, I would interpret them to mean that none of the varieties you tested contain the "positive" allele.