Your issue seems to fall into two parts, if I am reading correctly.
Firstly, you seem to be querying why a hint for THOMAS Gregory should be offered on the page of a WILLIAM Gregory. If you are referring to the WILLIAM THOMAS Gregory with an ID MX65-Y7J, the answer does not appear to be too difficult. The hint is for a TOM Gregory, and his marriage to Pinky Walker, who has already been entered as William Thomas Gregory's spouse on his Person page. The algorithm often picks up on middle names and, in this case, has found a match for a person who also married a woman of the same name.
Secondly, it might have helped if you had not been so quick in detaching the source - relating to Henry A Gregory - from Nanny A Gregory's record. However, I found the 1900 U.S. census record in question (see https://www.familysearch.org/tree/person/sources/LVYS-175), attached to "sibling" Henry A(llen) Gregory LVYS-175. The program worked perfectly well in offering this hint, as it transpires there was no such person as Nanny A Gregory! The original census record clearly shows the individual to be a male ("son") and (perhaps not so clearly) his actual name to be HENRY A Gregory - not the (female) NANNY A Gregory that was incorrectly indexed.
All that needs to be done now is to remove "Nanny A Gregory" - either by changing her sex and merging with Henry Allen Gregory, or detaching her from the parents. Either way, you will need to provide a detailed reason statement for your actions, of course.
(BTW - In the case of the latter issue, one with similar circumstances was reported here just a few weeks ago. Different family, of course and - in that case - the census did record the child's sex incorrectly, but the indexed female did turn out to be a male, the "female" having never existed.)
Thanks Paul. So you are saying the program is working "perfectly well." I did not look into the family because it is the second marriage, and I was going after the first marriage. I just pulled up the children to see if they were married and noticed the things I questioned about in this "Feedback." Thanks again, - Don