After getting Nanako pregnant by Rin and then staying at the Onsen Town inn to progress the pregnancy, some of her morning text talked about being "pregnant again" even though this was her first time. I opened the game in RPG Maker and had a look at the "Morning Dialogues" common event. Being pregnant by Rin is classed as a happy pregnancy, and looking in that section of code showed checks to determine a first pregnancy or not, then display the relevant dialogue. However, the checks are not entirely correct. They are currently set to "above" which seems to mean the same as "equal to or greater than". Changing the check to "bigger" seems to fix the problem.
In other words, lines that read: "FORK Optn:Varbl[0077:Times pregnant]-1abov"
Should really read: "FORK Optn:Varbl[077:Times pregnant]-1 more than"
Note that I've only tested the checks in the happy pregnancy section. I noticed there are also the same checks in the rest of the event code, so I assume these would need to be changed as well. Also note that I don't know if this issue is in the original database, as I'm only using the translated one.
Sorry for the rather long post for such a minor issue, but I try to explain these things in as much detail as possible.