No, Bella pregnancy event only fires if you have "BellaCum >=1" flag. And the only two instances where you can get it is; if you have sex with her during the garage scene in Ep 21 or if you cum inside during the night scene in Ep 23.Bella's pregnancy happens regardless of whether the MC had sex with her. I confirmed this on several saves from the beginning of the game, and a bunch more using the Start Any Episode feature. It's so consistent I am assuming it's a deliberate story choice rather than a bug. In other words, Donald is the father.
I suppose it's possible the pregnancy is fixed but who the father is will depend on our actions. That might be a way to inject a little last minute drama in some playthroughs while still having some low fat drama substitute for the others. I guess we'll find out when we finally see Episode 25.
I play with URM, so I am not making an assumption, it's literally what the code says.
Also, I just did a Jolina only run with the quick start from Ep 24 and I did not get the Bella phone call at the end of the ep. So it's probably a bug on your end.