Are misplaced, unused anchor bolts a problem?
Sloppy workmanship aside (could have been the mason or the carpenters), this probably isn't a serious issue. Anchor bolts are most critical in tornado and earthquake zones, but there are usually many installed, and a few that miss won't substantially increase the chance of disaster. 

The builder should at least cut them off neatly, flush with the concrete. They're ugly and a bit of a safety concern. If they won't do that, you can do so with a metal-cutting blade in a reciprocating saw or hack saw.

As a resolution I'd ask whether new bolts were drilled into the foundation when it was discovered that the wall would miss the original bolts. If not, you'll have to decide whether to pursue the matter in a legal sense.