I can only assume that Patricks father was Edward who died in 1866. Maybe Edward did not know his fathers first name
Thanks again for trying to solve this Rosie. I have even tried starting a Keenan tree to work my way through just that family line and I come to the same results without any alternative that fits the evidence.
Patrick would have been 4 when Edward died so it is conceivable that he could not recall his father's name. I have just had a thought and checked the 1871 census, Patrick and his two brothers, young Edward and Nicholas are living in their brother-in-laws house and his name is John O'Neill so that may be an explanation.
I have learned quite a bit from your help Rosie
Kind Regards
Edit: Patrick was 14 when his father died not 4 as I have stated (my bad counting). As he was living with his brother in law John O'Neill I would guess he is the "John" on the marriage certificate.