Can you eat squirrels and rabbits with bugs on them?

For some reason a lot of the rabbits and red squirrels I shoot around my house are full of bugs. I don't eat them when they have bugs but I don't know if it is good for you or not. I shot a rabbit last year that was full of bugs and I didn't eat it but I felt bad it had to go to waste. Even in the winter they were full with fleas and had ticks on their ears. Maybe I will have to butcher some of my own rabbits from now on. 
 
Yessir. Lyme disease is only transmitted through tick bites, not ingestion. It doesn't even transfer from nursing mothers to their infants. Bugs are lil protein flecks, they're fine. They should be removed when you dress the animal but any that are accidentally left on the meat somehow will be cooked or fall off during cooking. If however they have boils or herpes lookin sores on them then toss em.
 
One caveat would be that the insects (both fleas and ticks) are vector disease agents (here in Colorado there have been cases of Bubonic Plague), so it makes sense to exercise a bit of caution in carrying and cleaning the animals. I carry a plastic freezer bag in my hydration pack along with a set of rubber gloves. When I shoot the rabbit I don the gloves and field dress the animal on the spot (leaving the fleas and other insects in the field) and place the carcass in the freezer bag for transport back home for final cleaning and deboning.