Several GMO crop strains are specifically designed to produce pesticides or fungicides themselves, which offers more powerful effects and saves the effort of applying those chemicals to the growing plants. This is generally valuable for crop yields and profit margins, but it's appreciably different from external application.
The main concern is that producing these pesticides/herbicides inside the plant may include the chemical inside the parts we consume - you can't just stop application prior to harvest or wash off the surface before consumption. There's a lot of conflicting data here: the GMO designers have generally concluded that the chemicals are only produced in leaves/stalks and not the edible parts, but other studies have suggested that the chemicals might be getting passed on at levels which could be relevant to pregnant mothers.