Because you assume that gravity vectors can only add up. If you consider that external gravity is cancelled out by the gravity generated by the ship, there's no inconsistency.
You are assuming that gravity generation also equates to gravity nullification, this doesn't really follow, because if you nullify real gravity then you should also nullify the artificial gravity. If you are using some sort of field to nullify real gravity then it would also nullify the artificial gravity the ship itself is generating because it could only act by nullifying the field in that specific location and not the actual gravity generation source, because if it acted to nullify the source then the entire planet would be rendered without gravity. So if this is proper artificial gravity then the nullification would affect both because they are, well, identical in nature.
So since the planet gravity can't be simply cancelled out by the gravity generated by the ship, it would need to be nullified in some other way, maybe you are implying some sort of force field that blocks gravity, but then it wouldn't just work inside the ship, fields are spherical in nature and the gravity in areas around the ship would also be blocked because it would need to extend outside the ship to provide complete coverage.
But of course this also means your ship isn't actually affected by the gravity of the planet since you are cancelling that gravity, and rather than sit there on the ground it should just up and zoom away because the planet is moving through space at many hundreds of meters per second and there's now no force anchoring it to the planet, well apart from inertia keeping them together for maybe a second or so, and since the planets orbit is curved (well not in SC because they don't do that right?) the ship should travel in a straight line (because that's how it works right) while the planet moves on a curve, and the two would soon part ways. Well there's a lot of variables there depending on where on the planet you landed, because rotation of the planet and orbit of the planet will change how the ship behaves once you block out that pesky real gravity, maybe that's why they tend to blow away in the wind a lot?
I expect complications like this are one reason why ED steered away from artificial gravity, I mean it's all very well just saying "artificial gravity" to explain away why stuff falls to the floor in stations with no or micro-gravity, but if you want to model the actual physics of artificial gravity it becomes....complicated.
But of course that's not a problem for SC because they aren't actually modelling physics, either real or imaginary, in discernible way right?