Originally Posted by Albet
@mmorgan how did you guess that? I'm a newbie and still use troubleshooting software tools. For problems like this they are not much of help.
If the product is approximately 50 bp long it's likely that the 3' ends of the primers (which are usually 15-30 nt long) annealed together. When extension occurs, it generates a product of about 50 bp.
Most primer design programs will look for 3' complementarity as well as primer hairpin potential. I have used MacVector for primer design and it seems to be quite good. Many people swear by Primer3 which is available for free as a web interface.
Could you post the sequence of the primers you used??