I entered the name [name1], but the structure it gave me was really [name2].
I entered a name that violated IUPAC rules, and it gave a structure anyway!
The structure it gave isn't the one I meant.
Name/Structure is designed to give a correct structure based on the name entered. If you enter a name that is ambiguous, you're rolling the dice with regard to the structure you get back. For example, the explosive TNT is really 2,4,6-trinitrotoluene. If you enter "trinitrotoluene", however, you should not expect to get this structure. You might, but you might also receive the 2,3,4-, 2,3,5-, alpha,alpha,alpha-, or any of several other isomers. None of these would be incorrect for the ambiguous name "trinitrotoluene". If you want a specific isomer, you must enter a specific name.
In a similar vein, Name/Structure supports many types of nomenclature that are not condoned by any naming body, including IUPAC, IUBMB, and CAS. There is absolutely nothing ambiguous about a name like 5-chloropentane. The correct name for that compound would be 1-chloropentane, but that does not prevent Name/Structure from interpreting the name it was given and producing a reasonable structure based on that name.