Spaghetti squash is fine in any reasonable amounts in phase 1. Feeling bad isn't a normal part of SBD, so if you're feeling better it doesn't mean you did anything wrong. In fact, what might have happened is that you weren't eating enough good carbs to keep your energy levels up, and now you are. But the carbs you get from tomatoes (including no-sugar-added tomato sauce), spaghetti squash, etc. are good carbs. And the vegetables themselves are incredibly healthy in lots of other ways too. So do get a variety of vegetables, and don't worry about eating too many.
