Lewd Town Adventures is a SANDBOX GAME.
The DAY counter is not intended to be seen as ACTUAL DAYS that have passed since the start of the game.
The Prologue happens from Days 1-12.
3 years later - it's still Day 12.
Being a SANDBOX game, players are free to pursue every love interest in whatever order they like. While it's almost mandatory to progress ALL OF THEM at the same time, some players will likely neglect, forget about, or avoid some girls for whatever reason.
From the start, try not to take things too seriously. Do some women TALK ABOUT getting pregnant and then pop a baby belly the next day? Do some women discuss the POSSIBILITY and never get a baby bump? Sure. But that's for two main reasons:
1. They either are on birth control (as mentioned by at least one girl) and want to finish school, so even if you think they might get pregnant, they are not. OR they simply are not ovulating at the time of the creampie.
2. The time between creampie and baby bump may show as little as 2-3 "days" if you did not pursue them earlier in your playthrough, but in reality, it's been weeks for them.
This is the challenge of doing a Sandbox format with life changes that IRL take months. If players progress everyone at the presumed rate, it makes sense. But - being a 'free roam' style game, players are free to choose who to interact with for the most part, and that sometimes may make it seem like magic how long it takes for a girl to conceive or how short it is between insemination and third trimester.
Don't take it too seriously. Have fun. Especially because - in LTA - (on the good path mostly) the girls WILL give birth and MC WILL have children.