I believe that Emilio came up with this excuse himself because at the point that he has the discussion with Toycie about her being pregnant, his mother has not yet been told. Toycie meets Emilio at night to give him the news and his immediate response is that there is no way he could be the father because, as Toycie says,
"His body did not go into mine."
Horrified, Toycie tells Beka that Emilio does not believe he can be the father. Beka is horrified because Toycie and Emilio have been together for two years, "messing around" -- and she knows that Toycie has not been with any other men. Emilio makes things even worse by telling Toycie he won't marry her because if she has been fooling around with him for so long, she would do the same thing after they are married.
A real nice guy, huh?
Emilio and Toycie are from two different races, so the situation with them is symbolic of the Panias vs the Creoles, the Panias ill treatment of the Creoles.