Praise be to Allah.
If she was certain that she had seen the tuhr (sign of purity i.e., that the menses had ended), either complete dryness or the white discharge by which women know that the end of the menses has come, then any blood that appears after that is not regarded as menses, so it does not mean that she cannot pray, fast and have intercourse.
But if you were not certain about the tuhr, rather you based it on the usual end of your menses, then the blood was menses, because the period may be longer or shorter than usual.
Shaykh Ibn Jibreen (may Allaah preserve him) was asked:
What is the ruling on the blood that appears on days other than the monthly period? My period is usually nine days but in some months I bleed on days other than the days of my period, but it is a very small amount of blood, and it may last for a day or two. Do I have to pray and fast during that, or make them up?
He replied: This blood that is extra to the period is bleeding from a vein and is not counted as part of the period. The woman who knows the nature of her period should, during the time of her usual period, not pray, fast, touch the Mus-haf or let her husband have intercourse with her in the vagina. When she becomes pure and her period is over, she should do ghusl, then she comes under the same ruling as women who are pure (not menstruating). If she sees a little blood or yellowish or brownish discharge, that is istihaadah (non-menstrual bleeding) and it does not mean that she cannot pray and so on. End quote.
Fataawa al-Mar’ah al-Muslimah (1/277).
With regard to what took place of intercourse, there is no sin on you for that, because you thought that the period had ended.
There is no sin on the woman if she delays ghusl for janaabah so that she can do ghusl for menses and janaabah together, although it is better for her to do ghusl for janaabah, because by doing so it becomes permissible for her to read Qur’aan, as the one who is in a state of janaabah is not allowed to read Qur’aan, whereas the menstruating woman may read Qur’aan.
This has been explained in the answer to question no. 2564.
And Allaah knows best.