Hi,

Although there is no such notification regarding the discrepancy of thumb impression and what are the necessary steps that will be taken by NTA, but from a common sense point of view, I don't think the finger imprint will be matched with your digital print of your aadhar. As from some of the articles of fingerprint sensing, such cases can cause discrepancies and variation. So you have nothing to worry about this, I don't think it will create a problem although there is no official grounds of saying so.

Most often whenever the thumb impression is not prominent the authority would check the impression provided by you during your application form fillup. However since two of your thumb impressions were overlapping that will not cause any serious issues only if the other informations are correct.

Hope this helps

Wish you luck