We bought a lemon tree, then we were told we had to destroy it because it wasn't licensed.
This implies that you brought a ready-grown tree. Maybe only a few kilos, but that still takes a year or so to achieve, so they're relatively expensive. (This reminds me to water the 2m tall lemon tree sitting in the living room window, which we started from a seed in 2006. With pot and soil, it's over 30kilos.)
It just wanted to self-replicate and make us free food.
This, on the other hand, implies that you grew the tree from seed, or from a cutting of an original tree. The seed is one case, and is one of the reasons that plant breeders try to develop seedless versions of fruit, or ones with a very low germination rate. The propagation from cuttings though is much easier to contain, because you need access to the tree, not the fruit.
I was at the garden centre with the wife this afternoon. Many of the plant cultivars which the wife wanted to buy carried notices barring the buyer from propagating them without getting the prior written permission of the rights holding company. Buying those would have constituted accepting the terms of the contract, so I steered the wife to other cultivars from other suppliers which didn't carry such warnings.
I suspect that you brought a lemon tree from somewhere, and in the process agreed to a similar "no propagation" contract (did you actually read the terms of the contract that you entered into?) ; then you propagated the lemon tree to produce a clone (yes, a "clone", in the sense of "clone"). In doing so, you violated the terms of the contract you'd entered into with the selling company. And they complained to appropriate authorities ,who forced you to comply with the terms of the contract into which you'd entered.
(Your local laws and contract law may differ. But I suspect there's something along those lines happening. It's possible you did it from a seed, and the laws you have are even more restrictive than we have to deal with here. If your contract law allows you to be held to the terms of a contract that you're not shown ... it'll be almost like software sales.)