It's not an issue. "+" is not a function in Prolog. So, for example, X = 1 + 1 means that the term 1 + 1, or +(1,1), is bound to the variable X. It doesn' t mean that 1 + 1 is evaluated, and its result assigned to the variable X. Prolog doesn't have assignment, and all its data structures are immutable, including variables, so once a variable is bound it stays bound for the scope of the current execution branch. That's unification.
The thing to keep in mind is that Prolog borrows its syntax and semantics from (a fragment of) First Order Logic, and that's where its treatment of functions comes from. In FOL there's a concept of a "term": a variable is a term, a constant is a term, and a function symbol followed by one or more comma-separated terms in parentheses is a term. So if f is a function symbol, f(X,a(b), c) is a term, where X is a variable (in Prolog notation where variables start with capital letters or _). Terms are mapped to functions over objects in the domain of discourse by a pre-interpretation (long story). Terms are arguments to atomic formulae which look exactly like terms with one or more arguments, except they have predicate symbols rather than function symbols, so if p is a predicate symbol, then p(f(X,a(b), c), d, 1, 2, 3) is an atomic formula, or atom.
There's a bit of terminological confusion here because Prolog calls everything a "term", including atomic formulae, and it calls its constants "atoms", but, well, you learn to deal with it.
The difference between terms (in both Prolog and FOL) and functions (in most programming languages) is that terms are not evaluated and they are not replaced by their values. Rather, during execution of a Prolog program, variables in a term are bound to values, by unification, and when execution is over, if you've got all your ducks in a row, all variables in your program should be bound to some term with no variables, and all terms be "ground" (i.e. have no variables).
That's because a ground term is essentially a proposition, and so it has a truth value of true or false. The point of FOL and of Prolog, and every other logic programming language is to carry out a proof of a theorem, expressed as a logic program. If a term has variables we can't know its truth value because it may correspond to a different value of a function, depending on the values of its variables. So to know the truth or falsehood of a term we need to ground it. Unification in Prolog is a dirty hack that allows the proof to proceed without fully grounding terms, until the truth of an entire theorem is known, at which point everything becomes ground (or should be ... more or less, it depends).
ASP (Answer Set Programming) instead starts by grounding every term. Then, it basically treats a logic program as a SAT formula and uses a SAT-solver to find its truth or falsehood (it does more than that: it gives you all models of the theorem, i.e. every set of ground atoms that makes it true).
And that's where the tiger got its stripes. Don't expect Prolog (or ASP for that matter) to work like other languages, it has its own semantics. You don't have to like them, but there's a reason why everything is the way it is.
The thing to keep in mind is that Prolog borrows its syntax and semantics from (a fragment of) First Order Logic, and that's where its treatment of functions comes from. In FOL there's a concept of a "term": a variable is a term, a constant is a term, and a function symbol followed by one or more comma-separated terms in parentheses is a term. So if f is a function symbol, f(X,a(b), c) is a term, where X is a variable (in Prolog notation where variables start with capital letters or _). Terms are mapped to functions over objects in the domain of discourse by a pre-interpretation (long story). Terms are arguments to atomic formulae which look exactly like terms with one or more arguments, except they have predicate symbols rather than function symbols, so if p is a predicate symbol, then p(f(X,a(b), c), d, 1, 2, 3) is an atomic formula, or atom.
There's a bit of terminological confusion here because Prolog calls everything a "term", including atomic formulae, and it calls its constants "atoms", but, well, you learn to deal with it.
The difference between terms (in both Prolog and FOL) and functions (in most programming languages) is that terms are not evaluated and they are not replaced by their values. Rather, during execution of a Prolog program, variables in a term are bound to values, by unification, and when execution is over, if you've got all your ducks in a row, all variables in your program should be bound to some term with no variables, and all terms be "ground" (i.e. have no variables).
That's because a ground term is essentially a proposition, and so it has a truth value of true or false. The point of FOL and of Prolog, and every other logic programming language is to carry out a proof of a theorem, expressed as a logic program. If a term has variables we can't know its truth value because it may correspond to a different value of a function, depending on the values of its variables. So to know the truth or falsehood of a term we need to ground it. Unification in Prolog is a dirty hack that allows the proof to proceed without fully grounding terms, until the truth of an entire theorem is known, at which point everything becomes ground (or should be ... more or less, it depends).
ASP (Answer Set Programming) instead starts by grounding every term. Then, it basically treats a logic program as a SAT formula and uses a SAT-solver to find its truth or falsehood (it does more than that: it gives you all models of the theorem, i.e. every set of ground atoms that makes it true).
And that's where the tiger got its stripes. Don't expect Prolog (or ASP for that matter) to work like other languages, it has its own semantics. You don't have to like them, but there's a reason why everything is the way it is.