It's probably just a plain case of good luck/bad luck, but let's see the possibilities anyway:
Dondozo's catch rate is the same in both games, so that's not why. However, Legends Z-A has slightly different capture mechanics than S/V. The only things in Z-A that make it harder to catch a Pokémon are:
- The Pokémon being an Alpha. Alpha Pokémon have a 0.5x multiplier on the catch rate.
- You being Low-Rank. If you have a low rank, catching high level Pokémon is significantly harder. (from 0.7x to 0.1x) This is of course done to stop you from catching something over leveled early.
If the Dondozo you caught was affected by any of these things, that would explain it. There are no critical captures in Z-A, so if you used a critical capture to get your S/V Dondozo, that would explain why it was easier. Also, Catching Power Sandwiches exist in S/V, so if you used one it would also explain why it seemed easier in S/V.
If none of these things apply to your situation, you probably just got lucky in Violet or unlucky in Z-A. Of course, you could just be using different Pokeballs, or if Dondozo was affected by Status/Low Hp in one game. If you have any specifics on exactly how you caught your Dondozo in Violet or in Z-A, it could help narrow things down.
Hope I helped.
Source: Rotomlabs.net