Apologies if this has been reported already or fixed in a later version (playing the 0.3part2 Free), but in prologue2_emily_love.rpy when Emily asks if you've been fooling around with April, all the menu items are behind the if(a_secret_lovers) conditional. So if Emily already knows (either from the truck ride or the earlier threesome), it just skips past in a slightly jarring way.
Edit: Also the choices where you admit it set the e_secret_lovers variable to False, when it probably should be setting a_secret_lovers to False instead. (Further edit: As it is right now, if you admit your relationship with April to Emily in prologue2_emily_love.rpy, then the dialogue in prologue3.rpy at lines 793-817 and 904-925 will be the opposite of what it should be; Emily being shocked at the reveal that you're with April when she already knows and April not being shocked at the reveal or your relationship with Emily when she shouldn't have known yet. If you do fix this though, you'll want to move the $ april_harem = True outside of the if statement or else it won't get set when it should.)
Also also at the start of prologue3.rpy when the MC and April arrive in the city, there's a if(aprilislover) with dialogue followed by an else with alternate dialogue, neither of which makes sense if the MC is not sexually involved with April. Should probably change the else to if(aprilisasub), and also move the "Damn you are fine though."/"Thank you." lines that are right after it into the blocks of conditional text instead of after, since it also wouldn't really make sense if the MC isn't involved with April.
Edit #whothefuckknows: In pro4_intro.rpy, there's a handful of extra dialogues behind the emily_bi variable, but it's not actually possible for this variable to be True. If you choose the threesome in prologue2_emily_love.rpy/prologue2_emily_sub.rpy, it sets emily_bi (and april_bi) to True, but then immediately sets them back to to False in prologue2_3some.rpy. And Lancy foursome in prologue3.rpy doesn't set it either.