Hi Zoe,
If the variograms look OK, it's very unlikely that the sizes of the home ranges are being overestimated. I think you likely have a relatively small effective sample size for these individuals with fewer fixes, so just looking at the actual locations, there is a lot of area within the home range estimate that does not have locations. If you were to keep collecting data for those individuals, you will see more and more of this area containing locations.
When effective sample sizes are small, the bigger danger is actually underestimation of home ranges. When this is a concern (typically, an effective sample size < 10), you can use bootstrapping to improve the estimate.
For more info, you can read these papers:
Jesse