Chapter 1: His father apparently ran off with a younger woman. (This might be elopement or something else)
Chapter 13: We get a dream flashback of Hiroto and his sister being very affectionate siblings until her mother died. Hiroto does not know why he is being blamed for her death.
Chapter 21: This deals with Loa, and ghost powers. A ritual just before someone dies creates an item that has power, but no body should be able to contain more than one soul.
Chapter 29: We learn that the only ability his step-sister had was Reflection until later in life. Her additional abilities (and power) came from nowhere. She is said to possibly be the second S-Class.
Chapter 58: Hiroto is actually the only S-Class on ranking, with a code name of 'Calamity'. Also, there was a reason why the 'Ability Zone' was made (the city).
So, we know that Hiroto's gift is way stronger than he believes, and we don't know how far his actual ranking is known.
We also know that his sister somehow got two new abilities that are very strong, but her original is Reflection.
We don't know how she got her powers, but. . . and this is a theory. . .
There is a strong chance Hiroto's Hacking Ghost was recorded after causing the mother, and possibly father (I'm unsure if we got confirmation that the dad is alive), to die by accident. His sister possibly used reflection unconsciously to rebound the power, and it went to her. So Hiroto is left with his knowledge that the only power Hacking Ghost seems to have is the ability to interact with ghosts. Hiroto might actually have a stronger ability to instantly 'kill' someone by ripping out their soul, or just the ability to rip out the power from a soul and use it as his own. This is why he is an S-Class, his power pool is essentially enormous since he could just murder people for power, if that is what they know.
Alternatively, maybe the sensors trip on the fact that the ghosts are around him constantly. But it is odd that his power doesn't have an off-state, there is no will. Kind of like Ichigo from Bleach had the power to see ghosts constantly because he was always expressing his power. There is no activation requirement, but every other power we see used tends to have some way to activate it. It does suggest that the ability to see a ghost is a secondary requirement to use his actual power set. Well, that and being labeled a calamity, anyway.
Either way, something about how the mom died suggests that Rei did not yet have the ability to Undo it, or the condition to undo it wasn't met. Either Hiroto accidentally killed her, or Rei accidentally killed her by proxy by either reflecting an ability or gaining Instant Death without knowing. Assuming she doesn't have to say Instant Death or Undo to use either ability.