It's not exactly about caution, it's more about simplifying the system to help narrow down the cause of the problem.
Although there is some need for caution with carbon. Carbon will make your water more clear, or less yellow/green, allowing more light penetration. Imagine if you swapped in new bulbs after 14 months and began running carbon on the same day. That could possible cause some lightening in your corals due to the increase in PAR and light penetration.
In addition, I don't know exactly what carbon removes from the water, I know it's impurities of various sorts, could it possibly remove something that your sps need? I'm not entirely sure but it can be good to rule that out if you're having problems in your system.