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The primary disadvantages are the costs associated with the health of the herd. The producer may experience cows that can go down with milk fever or ketosis, or have to have some animals that require C-sections because a female was bred to the wrong stud and ended up with some larger offspring to birth out than was intended.

Other disadvantages include increased number of females that are needed to be bred at the same time, which often require AI, because the costs of keeping a sire is too expensive in relation to the costs required to care for, manage and feed females livestock. Mix-ups, like what was mentioned above, due to human error, are also concerns. Record keeping is a must, and can be a bit tedious if they aren't kept up to date. Special facilities must be built to separate females that are needing to be bred from those females that are pregnant and those that are birthing (this is especially true in swine housing). For dairy cows, this is also the same, with an additional facility or corral needed to house cows that are drying up before they have a calf, and for those that are being culled and sold off the farm. Costs in building and maintenance can stack up, as a result.

Another disadvantage is that, in intensive production, one person can't do all the work, so more money must be handed out for hired labour to help with the care, breeding and birthing of livestock. The producer expects his hired hands to do what he expects them to, but there are many instances of hired hands slacking off or doing something that they're not supposed to. This is a big risk the producer has to take when hiring people to help him raise his livestock.

So all in all, the main disadvantages a producer faces when breeding and raising livestock intensively are vet bill costs, maintenance costs, record keeping, and risk of hiring the wrong people for the job.

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