How are the gaps filled in images captured by CCD arrays?
In general, the common practice is to dither exposures and fill in the gaps. The dither serves multiple purposes:


provides some exposure in the gaps between the CCDs
smooths out pixel-to-pixel variations in the response.
prevents one bad pixel from ruining an entire observation


The dither pattern varies from telescope to telescope. For example, the following image shows the dither pattern of Chandra telescope.



Image from havard.edu

The effect of dither is removed during high-level ground processing of the data.