I had a damp crawl space partially caused by condensate dripping from an air handler. To fix my problem, which had caused some mold growth on the floor joist, I installed plastic on the dirt, closed the vents and installed a dehumidifier which I set on 38%. After about six months I noticed gaps in my hardwood floor. Could this be caused by drying out my crawl space? Could attempting to dehumidify the crawl space to 38% instead of 55% have contributed to the problem.

Yes.
The hardwood had been exposed to elevated moisture content "wicking" through the sub-floor from the damp crawl space.
The reverse has now occurred, allowing the hardwood to shrink. Unless the gapping is signicant, the floor will probably expand again in the summer, no way to really tell at this point.

If it was just related to crawl space moisture, the boards would be crowned. Turn the dehumidifier up about 5%, to 45%. You did good by dehumidifying the crawl space.

The main cause for the gapping, would be the heater your running inside your home, drying the wood flooring..