The enzyme does not have star activity, so you may have some issues:

Your PCR fragment is not well purified.

Your restriction enzyme could be contaminated.

Your PCR amplification could have generated mutations in your target sequence.

Try to check one by one to solve your problem.

Regards

It's possible. But I cheked out the purity and quality of DNA extraction before PCR. And my positive control give me the result that I expected... So... I don´t know... 

Is it possible for you to sequence the fragment and follow the online software of phytoplasma classification

Camilo

I think that the different patterns that you obtained in the digestion could be for two reasons:

If you are working with DNA from infected plants, you have DNA from plants, bacteria and endophitic fung andi in your PCR reactions you can have non specific amplifications for different reasons (Tm, primers concentration, PCR program) that when you make your digestions you can obtain different patterns.

The second reason is because you have phytoplasmas from different groups and that can generate several patterns after digestion. However, check these possibilities.

Kind regards

Thanks for your answer, Jorge, I'll keep in mind your ideas.