YES, THERE ARE REASONS FOR THAT, FIRST IS THE PURITY OF THE DNA YOU ISOLATE, MAKE SURE IT IS FREE FROM RE INHIBITORS. BEST WAY TO AVOID THIS IS TO USE HIGH CONCENTRATIONS OF DNA AND IN LOW VOLUME, THEN IN THE REACTION, DILUTE THEM. OTHER REASON THAT RESTRCITION ENZYME CANT CUT IS ALSO THE METHYLATION SURROUNDING THE RESTRCTION SITE. HOPE THIS HELPS.