Why won't my pokedex retain new information?

Why won't my pokedex retain new information?

Recently, my brother lended me his Pokemon Crystal version so I could have my own save file on it. I figured if it was my game for a while I would try cloning his Pokemon over onto my new file. I do not believe it worked the first time, and the second time I waited to turn off the game until the "Saving...DO NOT TURN OFF THE POWER" box was completely up and the music paused. When I opened the game his file was gone... There was no continue option (which was fine because I had his permission to have my own save file). The more I played it I finally looked at my pokedex and saw "Seen 113"(which fluctuates) and "Owned 86". It doesn't register my starter Pokemon and lists Pokemon I haven't seen or owned as just that. I noticed this while doing the Mr. Pokemon quest at the beginning of the game. Then after the Ruins of Alph I had caught an Unown and it listed for a few moments as caught in the pokedex (this same thing happens with other Pokemon I catch, like Caterpie or Hoppip), but when my pokedex was upgraded for the Unown setting it glitched. The Unown wasn't listed as caught and took on weird sprites from the Pokemon around it in the pokedex, and sometimes looking like variants of MissingNo. I clicked on the Unown pokedex and for a moment or two it was a glitched screen and then it restarted my game with the "this is for the gameboy color" message.

If it helps, my brother said that he was using the game for trading earlier. The pokedex doesn't have a lot of consistency, but it has the Johto AND Kanto versions. Some Pokemon listed as caught (that my brother doesn't remember ever getting in the trades) include Mew, Ho-oh, and Tyranitar. I looked in the PC and it lists that there are 0 Pokemon in the boxes (I checked this at the beginning of the game to see if any Pokemon actually cloned).

Any knowledge or advice on the situation would be helpful, and thank you in advance!