Tosfos asks the question in Kesubos 6B and answers that Shmuel was able to impregnate a woman without rupturing, while most men can have intercourse but can’t impregnate in such a manner
וי"ל דשמואל היה יכול לבעול בעילה גמורה שאשה מתעברת בו בלא דם אבל בהטייה אין אשה מתעברת ולהכי בההיא דחגיגה ליכא למיחש בהטייה אלא לדשמואל
We can answer: That Shmuel was capable of conducting a complete coitus that could impregnate a woman without removing any blood. That is highly unusual and the Gemara concludes that there is a greater likelihood that a betulah became pregnant in a bath, but when penetrating at an angle that is discussed here, which most men are capable of doing, a woman cannot be impregnated. Therefore, that Gemara in Chagigah which is discussing a betulah that was impregnated we need not be concerned with the possibility of penetration at an angle because that type of cohabitation cannot impregnate a woman. Rather, it discusses cohabitation similar to that of Shmuel,3 who was capable of even impregnating a woman without removing any virginity blood. It is only that type of cohabitation that could impregnate her while remaining physically intact. It is in reference to Shmuel’s cohabitation that the Gemara concludes in Chagigah that “Shmuel is different for he was extremely proficient”. (Sefaria)