Some restriction enzymes are very fussy about cutting in pcr buffers which often contain many different salts. Bfa1 is a poor cutter in pcr buffers generally. What taq are you using to make the pcr product and what volume of amplimer are you cutting and is it purified product or just amplimer in taq reaction mix? Are you adding additional Bfa digestion buffer if you are cutting unpurified pcr product?

In lane 2 and 4 you have a degradation of your gDNA. it is caused by the star activity of your restriction enzyme. To avoid this you should:

- decrease the number of units to µg of DNA ratio

- optimize the incubation time of the reaction . At extended incubation times, the restriction enzyme starts to cut sequences that are similar to its known restriction site into your DNA.

You must ensure the purity of the PCR product and check the temperature and incubation time of the restriction enzyme

If the restriction sites are outside (3' and 5') your PCR-product should contain some nucleotides (~6 nt) so that the enzyme is able to detect its cutting site. I had the same problem once due to poor primer design ;)

You should purify your PCR-product e.g. with ExoSAP and use a suitable buffer for your restriction enzyme. Besides check the temperature and incubation time. I also would recommend to inactivate your enzyme by heat to avoid star activity.

Your PCR product does not seem to be of the right size, check your primer sequences and try to sequence the PCR product to ensure it is the desirable product. Gel purify the PCR product if correct and digest with the enzyme. Your genomic DNA digestion also looks strange, it is more like a degradation. Hence, it does not show the enzyme is working properly.