The spots are due to sunburn. When looking at the plant you may notice that the spots are on the upper part of the fruit or leaves. The clematis may be getting too much sun where you planted it. The basil is happiest with a little afternoon shade such as under the canapy of leaves of the tomato plant. the tomato fruit is perfectly good, just cut away the brown portion and DON'T remove leaves from the plant as they help shade the fruit.