You're generally supposed to file a 12(b)(6) before an answer or, in some jurisdictions, at the same time. However, there are other reasons for motions to dismiss, like procedural reasons, mootness, as sanctions for misconduct during the course of the litigation, and many others. If they did blow this by filing the answer first, there are probably still other dispositive motions available. Jurisdiction, for instance, can generally be raised at any time, because any actions by a court without it are null and void although a party can generally implicitly waive things like defects in service of process by proceeding with substantive pleadings. This is less purely technical now than it used to be where you would have to plead formally something like a "special appearance" and if you didn't, you could inadvertently waive your rights.
The worst I could see is having to wait until discovery is over to file a motion for summary judgment instead, which could be a costly slog.
Note, one possible alternative dispositive motion is the less commonly seen 12(c) motion for judgment on the pleadings, which can be filed after the pleadings, and which can be used to raise most of the same issues as a 12(b)(6).
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