The bots are a major problem with this game at times, yes. But it's not true that work with the opposing team, it's simply not how they work. They're generally pretty random, tho definitely have a preference to target the player.
It definitely can feel that way when your bots basically give up and suddenly the enemy bots massively flank and you lose all your beacons and lose the game shortly after. But it happens to your opponents too, equally. Most people just don't notice when it does. The main problem I have with bots tbh might just be the ridiculous killstealing in FFA, they're so good at stealing your kills and then you die to spending half your ammo and 1/3 your hp trying to kill someone, deal fatal damage but some bot gets the kill instead.
Not to mention how sometimes in FFA a random bot will go on a rampage and get loads of kills, and end up winning the game, somehow beating out players with actual meta hangars.
The bots also have much stronger equipment than you most of the time (apart from at max), in terms of rank and levels not actual effectiveness, so you just can't really brawl with them. This is to make up for their incompetence, to be fair.
Then bots obviously have the remaining issues, such as always knowing where you are, and being able to aim completely irrespective of their actual facing direction..