If one doubts about whether a woman has started seeing menstrual blood or not, she is treated as not being in her menses. However, if it is after menstrual period (assuming that her period lasts for less than 10 days), because of seeing certain signs of being in menses, she doubts whether her period has ended or not, she is treated as being in her menses. Hence, in the given situation, there is objection in having sex.
Index:
Some grand religious authorities’ answers to this question are as under:[1]
Grand Ayatollah Khamenei (may Allah grant him long life):
It is not permissible to have sex when wife is in her menses. If he has sexual intercourse, it will make kaffara (penalty) mandatory but if they have no knowledge of the menses (and they have sex), they would be under no obligation.
Grand Ayatollah Makarem Shirazi (may Allah grant him long life):
If no blood is seen, there would be no problem in having sexual intercourse.
Grand Ayatollah Saafi Gulpaigani (may Allah grant him long life):
If they have doubt whether the woman has started seeing menstrual blood and they have sexual intercourse, there is no problem and they will not be liable to kaffara also.
Ayatollah Hadavi Tehrani (may Allah grant him long life):
Insofar as they are not certain that the woman is in her menses or when a woman is not in the days of istizhar[2], there is no problem in having sexual intercourse.

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