Hi, i asked about if Scully's baby was Mulder's baby as well but i got replies saying that it wasn't mulder's but Scully just told Mulder that it was his child. I don't get it. Did scully have Mulder's baby but pretended it was someone elses to protect it?

No, it was definitley Mulder's baby, but others might assume its not because of the miraculous situation it happened in.