OK, two questions here.
Hello and Welcome!
I'm not sure what to tell you about the knotty skin...I'm not sure if you can change that at all.
As for the worms you can try a water and soap solution to keep them off. Other wise you'll have to go around and pick them off every day. If you don't care about using insectisides you can try those too, but the soap to water solution is less harmful to the environment, cheaper, and will do the trick for the most part.
Next season when you plant your tomatos take a tuna or cat food can, cut both ends off and place it like a ring around the bottom of your plant. The worms can't crawl over the rough edges of the can so it forms a barrier to them climbing the stem. Of course you would need to have your toms in a cage with no limbs touching the ground once they matured.
No answer on the squash. Are you sure they aren't a different variety of squash and that's how they are supposed to be?