Hard to say without a picture to show the sizes of the fragments but possibly the bands are caused by partial digestion so the uncut plasmid shows different size bands for linear.coiled and supercoiled and maybe nicked plasmid dna. If the bands are small then you may be seeing star activity where too much enzyme(or the glycerol used to stop the enzyme from freezing in storage) find more cut sites than expected and give you unexpected band sizes

Hi,

Seems the sample you used for the double digestion contains many restriction sites with regard to the concerned enzyme used. I suggest you to use a good professional Restriction site mapper available online and check for the RE map and compare with your results. Personally I use NEBcutter, you may use as per your preference and laboratory you are working with.

Best of Luck!!

A picture would be very helpful. Have you tried each enzyme individually? That test might help parse out which enzyme is giving you the unexpected bands. BamHI is a bit notorious for off-site cutting. Sometimes a different buffer can help. I had this exact problem with a double digest of a pCAMBIA vector and the buffer change did fix the issue.

is the bamHI and sac I buffer compatible? when there is too much or not enough salt some enzymes start to cleave anywhere.... start with the restriction that need less salt /inactivate / adjust salt concentration / make the second digest. or have a look at NEB "HF" enzymes ...