Unbeknownst to Marcus (AKA Project : Angel) he is in fact a Skynet sleeper agent, psychologically programmed to lure John Connor and other members of the human resistance to their deaths.
According to Terminator Director Joseph "McG" Nichol, Skynet is now fully aware of the fact that Kyle Reese is John Connor's father and since Marcus is a T-700 'Infiltration Prototype' (created specifically for the purpose of luring John Connor into Skynet's clutches) he must have been fully briefed on the paradoxical nature of John's parentage including the fact that he may appear older or younger than his father.
Q: In the earlier movies, Skynet is not aware of Kyle Reese. So, why
are they aware of him now?
McG: It’s a function of their recon during the dark period, and a
function of their awareness of the events that had happened since Kyle
Reese traveled back. By virtue of John Connor being alive, that means
Kyle Reese did meet Sarah Connor and impregnate her. That data exists,
and was brought into the fold at Skynet.
Although Marcus might only be aware of this on a subconscious level it should
come as no surprise to hear John Connor talking about Kyle Reese as his father.