Same here, just noticed this today as well. Was using only metro towers. Wave 60-80ish only purple towers went to inv and money bins
I think you probably double tapped them for auto-transmute.
You can check by long pressing the towers icon in the stats screen of the game. There you can also undo auto-transmute.
And when double tapping, you can choose how many of this card you want to keep on your hand.
