I had a similar problem this winter. I had some largish tires (35 mm) that would barely fit on my old road bike. I used clip on fenders and there was overlap. To me it was more annoying than dangerous but YMMV. The fender hitting my foot never caused a crash but would press the fender up against the tire. Since I was moving slowly it just made noise. Since they were knobby, studded tires, they made a lot of noise.
I prefer powergrips to toe clips for a variety of reasons and switching to them might solve your problem. To be honest, I never liked clips anyway and while I think power grips are OK, I'll probably move to something like shimano's A530s. With those you can use cleated or regular shoes. You can also get shoes where the cleats are recessed enough that walking on them is no problem.