I sent my Combusken out to fight and catch a Zorua and after catching it it gave the normal message that Zorua was sent to the PC. A few minutes later I finally noticed my Combustien (First slot) had been overwritten by Zorua and checking the PC there was another Zorua.
Now my starter pokemon is gone ;-;

Version?

The latest one, Beta 4 on 1.10

Is this with all Pokémon or only with Zorua?

This is the first I've seen it happen. I've only caught around 10 Pokemon, it hasn't happened with any of the others though.

Oh and probably couldn't effect it but I suppose it would be good to note anyways, I'm using both forge and liteloader to be able to run zans minimap along with pixelmon. Thats it though, no other mods.

Update, Zorua was bugged and wouldn't heal after stopping at a pokemon center. Didn't notice until I entered a battle with it which is when Combusken came back out but in my pokemon party it still showed as Zorua. I couldn't battle or run or use my bag. I could only check my team (all of which were dead so I couldn't try switching pokemon) so I had to force quit. Reload and I have my Combusken back in my party as normal (thank god).

I am experiencing this same issue on beta 3. It happens almost every time I catch a pokemon. I have to disconnect from server and reconnect to fix it every time. I have tried to get around it by using several different pokemon in the first slot, using different pokeballs, catching different pokemon, and changing the box on pc. It has happened at least 10 times.

Im not sure if this helps, but I am also experiencing a few other bugs that may or may not be related. (1) Client crashes after equipping armor. Have reproduced using diamond, sapphire, and ruby armor. After crashing I cannot stay connected for more than a couple seconds unless I manually delete player data. (2) When attacked by wild pokemon, sometimes the battle never starts and I have to close the client completely to continue. I can see the battle menu but I cannot battle, run, change pokemon, or open the menu (ESC).