It can mean that your primers were not designed specifically. When you design your primers you usually never get a perfect set for the first try. They can also amplify through self-dimerization.

You should blast your target sequence to see similarities in different species.

Also, you can try increasing the temperature. If you lost all amplified signals, your primers are not good.

Sometimes this can happen if primers are designed within exons of genes. Gene sequences are usually highly conserved between species while intron and intergenic sequences are free to mutate without consequence so are much more variable so more useful in distinguishing between samples of different types

If you know the loci where there are differences. Then using the primers available, you can identify patterns. If you are dealing with breeds, varieties or cultures of microorganisms, then this is not suitable for identifying patterns.

Regards, Sergey