A nondeterministic PDA for any triple $\langle q,a,A\rangle$ may have more than one moves/transitions and so the NPDA may have different computation paths/branches depending on what choice the NPDA makes (see this definition for details). So, for any input $x$ if at least one of these sequence of choices leads to an accepting configuration then we say the NDPA accepts $x$. In this case whether or not other possible computation branches lead to an accepting configuration does not matter. At least one accepting path is enough to accept the input $x$.
Now, regarding the question in your comment:
Now what if that one branch is the one which accepts the prefix of the language ? What happens to other branches?
You presumably mean "the prefix of a string", in particular, say $x=aaaaa$ and its prefix $y=aa$. For a NPDA $x$ and $y$ are two different inputs, the NPDA may accept or reject both strings or accept only one of them. This absolutely has nothing to do with the prefix property of a language.
Example: a PDA accepting the set of odd length $a$s and and empty string.
The basic idea is to keep track of how many $a$s are read, even or odd number of $a$s, using the stack symbols.
$\delta(q,a, Z_0) = (q,Z_{odd})$
$\delta(q,a, Z_{odd}) = (q,Z_{even})$
$\delta(q,a, Z_{even}) = (q,Z_{odd})$
$\delta(q,\epsilon, Z_{odd}) = (q_1,\epsilon)$
$\delta(q_1,\epsilon, Z_0) = (q_1,\epsilon)$
$\delta(q_1,\epsilon, Z_{even}) = (q_1,\epsilon)$
$\delta(q_1,\epsilon, Z_{odd}) = (q_1,\epsilon)$
This PDA is not deterministic due to the following two transitions:
$\delta(q,a, Z_{odd}) = (q,Z_{even})$
$\delta(q,\epsilon, Z_{odd}) = (q_1,\epsilon)$
In other words it has two choices when it is in the state $q$ and the topmost stack symbol is $Z_{odd}$.
Now suppose this PDA reads $aaaaa$. After reading the third $a$ it may enter the state $\delta(q,\epsilon, Z_{odd}) = (q_1,\epsilon)$ which will empty the stack but the rest of the input are not read, and so this branch does not accept the input. However, the PDA has another choice, namely $\delta(q,a, Z_{odd}) = (q,Z_{even})$ which leads to accepting the $aaaaa$.