I have a cannondale 2.8 aluminum frame and I think the rear triangle is bent a little. When I mount the rear tire I can get it centered but after riding a little it always cocks to the left a little.
The tire does not hit the chain stay but it is close, I think it might be the L/R drop out as the drop outs extend about a inch back from where the chain and seat stays meet. Is this something that can be fixed or os bending aluminum a no-no?

This problem is often a symptom of dropouts that are out of alignment. The inside dropout faces should be parallel with each other. A good shop should have the tool to check this. You can make your own with all thread, some nuts and some washers. If you decide to make your own, PM me and I'll show you how. This could also be the result of a loose skewer. The skewer lever should be set so that it begins to tighten at the 90deg position in it's 180deg throw. But check dropout alignment for sure. If this is an alignment prob, have a shop do the work to avoid voiding any warranties. Contact Cannondale if you run into resistance at the shop.

It is possible, but not extremely likely, the frame is off to that degree. It can be check by a good shop, see Frame Alignmnet. The dropouts can be out of alignment, and this would make a wheel trickier to get in, and will stress the axle. See also Dropout Alignment

If you have a replaceable dropout, double check it is properly mounted. These can sometimes prevent a wheel from centering.

Be sure to double check the centering or dish of the rear wheel. See Wheel Dish

i had that problem but discovered that it wasn't the frame..
It was the skewers.. It had somehow loose its grip when I pedalled hard or when I hit a bump..

After replacing the defective part, everything was well.