Or you may have the motor mounted to low which in turn, would have the chain slapping the chain stay of the bike, one of the reasons that my motor on my bike is raised a little higher than most builds here on the forums as seen in pic below...You will also notice that I eliminated the tensioner while I was at it and custom cut and fit both chains on the left and the right in order to work properly and be perfectly aligned.A photo of the bike will help. You may very well have a common frame where someone who had the same frame can speak on it. It is very possible you don't have the engine mounted correctly (leaning too far to the non-drive side of the bicycle) or the wheel isn't straight in your dropout. If the chain is hitting the tire itself then a thinner tire may be beneficial (such as going from a 2.125 to a 1.95)