Rather than simply speculating, we went right to the source: Honda. We asked the company's Automotive Public Relations person, Chris Martin, what was going on, and he said this:
The same new factory that was building the Fit for the last two years in Celaya, Mexico earlier this year began producing the all-new HR-V as well. As we worked to build up HR-V inventory for the U.S., Fit production suffered a bit. To add complication, the HR-V then went on sale in Canada and Europe shortly after the U.S. on sale, and those markets are also supplied from Celaya. Typically at introduction, we try to build up a significant amount of inventory in each market to help get the model off the ground. In this case, that meant reducing Fit production for an extended period of time. Since HR-V has been a run away hit, we are now taking steps to build additional Fit units in Japan, and the first of those units from Japan are beginning to arrive now. It may take a few months for things to settle back into a "normal" pattern, but we expect both Fit and HR-V to continue to grow sales over the next year.
So there you have it. It's been a supply issue, and Honda is tapping its Japanese factories to remedy it. For what it's worth, I've heard from a few Subcompact Culture readers that when the Fit first came out, dealers had scads of them on lots. However, now you're hard-pressed to find one on any of the lots, and now you know why. The good news is that if you want a Fit, the cars should become more readily available soon.