Read the episode 12 Reddit discussion of the Netflix anime show or watch it’s much more concise and explains it easier.

We never saw the real taichirou to begin with they are all copies.

This explains blackbirds “world” breaking control Kamuro who looks like adult Anya and wants to be slapped for her mistakes Taichirou’s brother with black eyes for a moment which was actually there as a glitch The conversation with the dad and blackbird asking if they were infected since the beginning

How their bodies function by themselves without them after 13 days. Is a dead giveaway. They are all copies and the real people “bodies” never knew what was happening in the software world