By default in that case the plugin will just pick the first available funnel and apply it.
But if you want to have more advanced logics, then use the “Funnel Priority” feature.
Set the priority score for your funnel from 99 to 1, where 99 is the lowest.
For example, you have funnel A and funnel B with the same product attached. Funnel A has a priority 1 and funnel B has a priority 2. When customer makes a purchase, he will see the funnel A, cause it’s priority is higher (equal to 1, which is the highest priority).
Alternative question: What happens if several different products in customer’s cart have separate upsell funnels applied to them? Will they see tons of offers? Or will the system prioritize and just pick a specified number of offers somehow?