When you press "mark known and delete", the same card pops up again, but when you press "mark known and delete" again you are actually marking the card that came after this card as known (though you cant see what kanji it is, because it just shows the same kanji as the first time)

Pretty sure the same thing happens to me
I reproduce this by:

1. Open up my recognition deck
2. Mark the card as known, and delete
3. The same kanji pops up, though I have already marked it as known and it should be deleted.

At this point, If I exit and go back to my deck overview and press the recognition deck again, the card is gone.

If I instead mark the kanji as known again, it will show a new kanji. If I mark this kanji as "Good", it will throw the error OP described.

This font needs to be larger, and preferrably a bit thinner. It is hard to make out all the strokes.