Why is sexual relations during menstruation forbidden? What if deep penetration is the cause for bleeding but one is convinced is menstruation?
Allah wants us to be mentally and physically pure. When people asked the question about menstruation, Allah mentioned in quran that it is kind of impurity and sexual relation is not allowed.
In the next verse, Allah mentions women as a sowing ground. Thus one reason of intercourse should be that too.
Normally women know about their cycles and its variations. It is always good that one should avoid sex when that time approaches. If for some reason there is some confusion, the Allah knows best and He is most forgiving.
Whenever in doubt, and if you think that you have transgressed Allah's boundaries, you can compensate it with prayer and charity.