Debra, you may want to wait for additional input from others because I think correction will require a kit deletion. From what I can decipher it looks like, last January 14, both kits were created, but your father's was uploaded first, about four minutes before the second kit was created. When your mother's data was uploaded, the file from Ancestry DNA that was used was actually the same raw data file as for your father. I don't think it has anything to do with the GEDCOM information or who is set as point person(s), but that the two sets of raw data are identical though designated as being different people.
I can tell the data uploaded for your mother is incorrect because I can see that the tokenized markers include almost 900 that are in the nonrecombining area of the Y chromosome.
Assuming you have both sets of raw data, the only recourse may be to click on the yellow pencil icon next to your mother's kit number on your GEDmatch dashboard. On the subsequent screen, the second tab near the top will be titled, "Kit Removal." Select that, enter your password to confirm that you control the kit, and then click "Delete."
Note: That step is irreversible. So be absolutely certain you're ready to do it.
Probably not necessary, but I would wait a day after the deletion before uploading the correct data file, just to give GEDmatch a chance to go through nightly processing and clear any lingering data cache. Then you'll upload your mother's data via the usual method, which will create a new kit number for her.
If you aren't certain about whether or not the raw data files are labeled correctly, you can always download them again from AncestryDNA. If you'd prefer me to look at the files you have on hand, you can send me a private message and let me know your email address. I'll then send you link where you can upload them securely--they'll be automatically encrypted--and I'll have a look. I can confirm which set of data is male and which is female, and I can make certain that the files are intact and not corrupted.
Downloading a fresh set of data from Ancestry will probably be the best (and fastest) route but, hey, I'm happy to help a new member if I can. 