Not able to replicate; I generated 12 from the encounter database with randomized IVs and it showed the same origin (via Static Encounter in Route 4) in both Gen3 as well as when transferred to Gen4.
Generally, when you transfer from Gen3->Gen4, you lose the original met location. PKHeX still has to iterate through every possible encounter until it finds a suitable match; without met location, the matching is one feature less strict (no met location check), so it sometimes it gives a compatible encounter from earlier in the iteration of all encounters.
If you upload your Gen3 Magikarp I can take a look and explain why. If it's a Method 4 Magikarp, then it's not legal.