One of my grandmothers was like that. Not only did she get me muddled with my female cousin, but with my aunts (her daughters) as well. I was Jill, Joy or Sibyl more often than myself.
Same here. A woman in the village and a teacher at school were forever mixing me up with a sister or cousin. I was too shy and polite to correct them.
The priest may have been used to seeing all 4 sisters together each Sunday and as there was a set of twins wasn't certain who was who. Perhaps, like the woman in my village and the teacher at my school, he'd been addressing Amelia as Ellen (or Mary Jane or Ann) or Ellen as Amelia (or Mary Jane or Ann) for years and hadn't been put right.
Alternatively the priest might have needed (new) glasses and couldn't read the mother's name scrawled on a slip of paper and guessed. Perhaps all he could make out was "el" and concluded the name was Helen. (Try writing "Melia" and "Helena" with your eyes closed.) We don't know how much time had elapsed before he wrote the baptism in the register. He might have done another dozen baptisms + a few weddings and funerals before he got round to writing it up.
I've been at a funeral where the elderly priest who'd known the deceased by his Christian name for 20 years, referred to him by his son's name.