I'm not sure if I've found an error or not, but this doesn't seem like it should've happened...

Before playing a game, I wanted to move mcd002 from slot 2 to slot 1, so I disabled slot 2 and changed slot 1 from mcd001 to mcd002. This should result in mcd001 being inactive and mcd002 being active in slot 1. But somehow, mcd002 decided to copy itself into mcd001, creating two of the same file and destroying all my data in mcd001. Is this a glitch?

If i want to change my memcards i always let mcd001 as it is and install another pcsx2 , enter the ps2 browser after the bios and sent everything to mcd002 and overwrite it with the mcd002 from my real ps2 folder.
I think its a problem for pcsx2 to change your memcards like that and read them after that.

somehow i had a similar problem , but it does occur when i "crash" the emu

it overwrite on the psx2.ini somehow , showing on the ini the same name on both memory cards mcd001
it does give an error of NTFS compression stream error , so you do need to change on the memory card option the 2nd slot back to mcd002

I usually use mymc to change the savegames i need if they're on a backup memorycard


Ps.: when i had the ntfs compression error , even if i had mcd001 and mcd002 files , it would assume that both memory cards were the same so dont know if happen to you giving you that error

This bug has been reported a lot. I'm looking into it.