Most companion planting content lists good pairings and stops there. The mistakes below are just as well documented but far less discussed, and several of them are common beginner combinations that look reasonable on paper.
Planting fennel near almost anything
Fennel releases compounds that inhibit the growth of many neighboring vegetables, including tomatoes and beans. It is one of the few plants with a genuinely long list of poor companions rather than just a few specific conflicts, and is best grown in its own isolated bed.
Crowding beans and onions together
Onions (and the allium family generally) can inhibit the nitrogen-fixing bacteria that beans rely on at their roots, reducing the nitrogen benefit beans are normally planted to provide to surrounding soil.
Pairing potatoes with tomatoes
Both are nightshades and susceptible to the same blight and pest pressures. Planting them together does not cause disease on its own, but it does mean any blight outbreak spreads between both crops rather than being contained to one.
Overcrowding "good" companions
Even genuinely beneficial companions like basil and tomatoes can hurt yield if planted too densely — the benefit of companion planting comes from spacing that allows both plants room to grow while still being close enough to interact, not from cramming as many companion pairs as possible into a small bed.