I also thought people were mixing up two different names, thinking Eleanor is pronounced the same way as Elena....
Eleanor Roosevelt is definitely Ellen-or isn't (wasn't) she?
If I hear an a at the end I "see" Elena and it wouldn't occur to me it was a pronunciation of Eleanor...
I'm also not young (hence Eleanor bringing Eleanor Roosevelt to mind not some recent actress or someone perhaps!)
Jess-ca probably is an accent thing but I don't like the sound of it either Duchess and would say Jess-i-cuh - I wouldn't have picked a name I didn't like a local or my partner's pronunciation of!
My kids pronounce their own names two different ways depending upon which language they're speaking, despite the fact we tried to choose names with only one pronunciation, and at work I get a totally different name from clients because my name is just gibberish to non English speakers!
Different pronunciations or even different names are fine imo except if they really grateful on you and are being used by the child's other parent. She might start calling herself Jess-ca!
I wouldn't "tell him he's wrong" but would discuss it, see if he knows he's doing it and prefers / likes Jess-ca and let him know that it sounds unpleasant to your ears, especially if he originally pronounced it differently and has swapped!