i dont think you understand how menstral cycles work, its less likely about 2 weeks after a period, the two weeks before and during are quite unsafe though. also it might not be explained in the manga, but she might be on birth control /shrug
i feel like this chapter wasn't suposed to have sex in it, or it was suposed to have another scene that led on to the act but the way it was done was kinda abrupt, from wholesome welcome back scene to sex scene right away