Praise be to Allah.
There are no consequences for your having repeated tawaf and sa‘i that you thought were required of you, then you found out that they were waived for you in the ‘umrah that you did to make up for what was lacking in your Hajj.
With regard to tawaf, it will count as supererogatory, because in the case of tawaf, there were be two intentions: the intention of doing tawaf in general terms, and the intention of doing tawaf for a specific reason, which is tawaf al-ifaadah. So if the intention of doing tawaf for a specific reason is annulled, there still remains the intention of doing tawaf in general terms.
With regard to sa‘i, there is no voluntary sa‘i that may be done independently of Hajj or ‘umrah; rather sa‘i is prescribed in the case of Hajj and ‘umrah only, as is also the case with regard to stoning the Jamaraat, and halting in ‘Arafah and Muzdalifah; none of these actions is prescribed on a voluntary basis outside of Hajj and ‘umrah.
See the answer to question no. 36869 .
Our advice to you is to focus on your own affairs and strive to do that which will benefit you, and ignore these intrusive thoughts (waswasah) about acts of worship or any of your affairs, for if they become entrenched in a person’s mind, they will soon spoil his religious and worldly affairs.
And Allah knows best.