Spelling of the surname depended on who gave the info and who wrote it down. In my yrs of Cain(e) research I find them used interchangeably. Sometime the same person, the same family will be spelled both ways at various times. One family who came to Missouri had one brother Caine and the other brother Cain--the descendants of each kept the spelling but all are from the same family.
So I wouldn't be too concerned about the spelling.
I have so many Caines in my database I made the decision early on to spell them all with the e so I have them all in the same section.