Always include a -RT negative control- This means, after DNaseI-digestion the RT-reaction is prepared with all components but the Reverse Transcriptase. use the same amount of this sample as for your cDNA. If you get a product in the -RT sample you know it is due to DNA-contamination. 

If there is no information on the whole genome level, to my knowledge it is not possible to rule out the amplification of repeated regions. But maybe someone else has an idea how to solve this issue.

Blasting the primer sequence will help but as a final check once you have your primers just amplify genomic dna and hope that they do not amplify anything

Thanks so much for your answers, they are really helpful

I used the blast for specificity and I got this message: Products on potentially unintended templates. What does it mean??

This means that your primers are not specific for the sequence you want to amplify. So there will be a mixture of pCR-products on the gel.

Thanks