The first is attribution. Commission is triggered by a tracked link, which means you pay whenever that link was involved, not whenever the affiliate caused the sale. A meaningful share of affiliate commission in many programs goes to interactions at the end of a journey the affiliate did not start, including coupon sites that intercept customers who were already buying. You are then paying commission on revenue you would have received anyway.
The second is control. Affiliates say things about your product that you did not write, and you are associated with wherever your links appear. For a young business still establishing what it stands for, that is a real risk, and the enforcement tools are weak because you cannot see everywhere a link is used.
The third is that it rarely works below a certain scale. Affiliates promote what converts, and a new business with no track record and modest volume is not attractive compared with established alternatives. Running a program that nobody joins consumes the setup effort for nothing.
Where it does work is where somebody already talks about your category to an audience that trusts them, and the arrangement formalises something that would have happened anyway. That is closer to a partnership than a program, and it is worth pursuing individually rather than by opening a general scheme. Start with three specific people rather than software, and only build the program if those three produce enough to justify it.
If you do run one, set the terms so they cannot quietly work against you. Exclude discount and coupon sites unless you deliberately want them, since those intercept buyers who were already converting. Define a commission window short enough that credit reflects genuine influence. And require disclosure, which is a legal obligation on the affiliate and a reputational exposure for you if they ignore it.
Decide the commission window and the attribution rule before anybody joins, because those determine what you actually pay for and they are difficult to change once people are earning under them. A ninety day window credits an affiliate for a sale they touched once three months earlier, and a last click rule credits whoever appeared most recently rather than whoever persuaded. Both are defensible and they produce very different costs.