Looking at individual players, you could be getting a small sample size effect. Factors involving your pitching staff such as ground ball/fly ball tendencies, strikeouts, etc. are going to impact individual defensive stats such as range factor.
For example: if you have a ground ball staff that also creates a lot of strikeouts, it follows that there will be less fly ball opportunities for your CF, thus leading to a lower range factor. That doesn't mean that he's not as good as the CF on another team . . . it just means he has less opportunities.
When looking at defense, pay attention to plus/minus plays. That will probably give you a better feel for your defense than will range factor.